The Underground
by TheMysteriousComicGeek
Summary: The Doctor gets abducted by an outside the government agency known as the Underground. Their goal: turn him into the perfect weapon. Warning violence and cursing. I am rewriting this story. So, it is under reconstruction right now and I'd rather you not read it, until this message is gone and everything in my opinion is perfect. I wrote a note to explain why, on my profile page
1. Prologue

This story will have quite a bit of Doctor whump. If you are squeamish don't read. Please review!

Prologue

A man stared out the window of an office building. Cold, blue eyes scanned the outside world, the people bustled about not realizing the danger that lurked about.

"Ignorant people,"he spat.

his body was rigid and his hands clasped behind his back. A snarl curved his lips. His gray hair was cropped close to his head and he wore green, military wear with combat boots. He turned on his combat boots and marched back to his desk. Awards were hung meticulously along his wall, many were dedicated to military achievements. His desk was organized with neatly stacked folders on top. Swiping a tan folder, He opened it, his eyes scanning a section on new tactics against the unearthly enemy. A knock sounded on the door.

"Enter," he barked gruffly to the knock, not looking up.

The door creaked,as a young private came in, his feet together and his chin raised. He saluted the older man, Colonel caught it from the corner of his eye.

"Colonel Graham, sir."

"State your business."

"Official business, sir," the Private stated," about project emerald."

"emerald."

"yes, sir."

Colonel Graham looked up from his work and over at the young man who stood in front of him. He slowly got up, smacking the folder on his desk. Clasping his hands behind his back, he circled the young man like a hawk to its prey.

The young man stiffened, eyes staring straight ahead.

The young private continued, "the man who's waiting down there said he found a solution to your problem."

Colonel Graham coldly nodded his head.

"Take me to him," Graham ordered.

"Yes, sir," the young man responded, he saluted and turned out the door.

They walked down the long hallway in stoic silence. The Colonels hands clutched behind his back. The hallway looked like an ordinary office building hallway, with light brown carpet and tan walls with a couple chairs and a fern for decoration.

The young man stopped at an elevator, he pushed the button, and the elevator slid open. The two men stepped inside both with their chins raised and hands crossed in front. The young man pulled out a card and slid it through a slot. A scanner popped out and he pushed his hand on top of it while a computer did a full body scan. There is a second ding and a computer face popped up.

"_**Welcome Colonel Martin Graham and Private Jason Green," **_it said in an electronic female voice.

"_**We will now go underground."**_

The computer face vanished and the computer slid back into the walls. A sudden jolt ricocheted through the elevator and it quickly descended down.

The computer popped out again.

"_**We have arrived."**_

The doors slid open and the two men step out. The walls were white-washed with clean white tiled floors. Doors were aligned along the hallway and people in white lab coats quickly walked by holding clipboards.

"Hello Colonel Graham," a woman stated.

Colonel Graham grunted a hello and marched his way down to his second office.

The halls had different doors on either side, labeling different labs. He turned another corner and a glass door was at the other end. He swiped a card through and the door blinked green before sliding open. He continued his march down the long hallway, Lieutenant Green following closely behind.

The hallway was lined with cells. Each cell was completely white with a bluish energy field in front. Some were occupied with the strangest creatures. Some of the creatures were green while others were blue, some had spikes while others had fur covering their whole body. Two scientist walked by with a gurney, a red creature with spikes was wheeled past, strapped to the gurney. The Colonel sneered when he saw the creature before turning quickly around another bend into an office. He threw open the doors which hit the wall with a loud bang.

A Man in his thirties was leaning back in a chair. His brown hair neatly combed and his green eyes holding knowledge of a plan no one else knew. His legs were crossed on top of the interrogation table and he was tossing a ball back and forth between his hands.

The Colonel growled and marched over to the man.

"Get out of my seat," the Colonel ordered.

The man threw his hands in the air as a sign of surrender and bounced up, making his way around the table. Colonel Graham sat in his seat, hands folded on the desk.

"What do you want?" he asked, his eyes calculating.

The man across from him smiled and plopped into the chair.

"I came here to make you an offer," the man stated.

"You said something about finding a weapon."

The man scratched at his chin.

"I did. You create super-soldiers out of non-humans, correct?"

The Colonel grunted an affirmative.

"Who the hell are you?"

The man across smiled smugly, his face contorting into arrogance.

"I'm the man who's going to get your weapon."

"What organization are you from?"

The man leaned back and put his hands behind his head.

"UNIT."

"The Underground does not associate with UNIT. UNIT is our enemy. Leave now or suffer the consequences of approaching me!"

"But don't you want your perfect weapon," the man asked innocently.

The colonel growled. The man grinned.

"That's what I thought."

The man reached into a black suitcase. He pulled out a nice laptop and flipped it open. He typed something into the computer and it began to buzz. The man flipped the computer around and the colonel lifted a quizzical brow.

"They call him the Doctor," the man explained, "He, apparently, is the last of his kind and he's looking for a home."

The man smiled wickedly as the colonel read through the Doctor's UNIT files, a grin steadily growing on his face.

"He's destroyed whole worlds,"the man added.

Graham looked up at the man in front of him, smiling, he reached out to shake the man's hand.

"I think you have yourself a deal," Colonel Graham stated, "Get this creature for me and bring him back here and in return I'll pay you two million dollars. I want this creature and you better not screw up or else."

The Colonel slid a finger across his throat as emphasis of what would occur if he failed.

The man brushed his hair back and smirked arrogantly.

"I'll get some of my best men on it. Next time the Doctor stops by, we'll bag him."

The Colonel shook the man's hand again before taking one last look at the file. From the picture the Doctor appeared to be a handsome, young, human man in his late 20's early 30's with wild brown hair and dark brown eyes, but Graham knew exactly what he was and nothing was going to stop him from obtaining the Doctor for his own personal agenda.


	2. Chapter 1

Please Review! I always like reviews!

Chapter 1

The sound of whirring echoed off the quiet streets of early, morning Cardiff, a blue box slowly begins to materialize and the whirring grew louder. A loud thunk sounded as the box lands, the whirring dies down. The blue doors slam open and a tall man steps out. His brown, tousled hair sticking straight up and brown eyes full of adventure and excitement, a large smile gracing his face. The man is wearing a long brown trench coat over a brown pinstripe suit with white trainers.

"Ahhh...Cardiff," he stated, he sticked his nose up into the air and takes a long sniff, sighing, "2015 Cardiff. Just a few years in your future Earthgirl!"

A tall red-headed woman, in a jacket, stepped out, blue eyes scanning the streets.

"Cardiff," Donna said, she gestured at the surroundings ahead, Whole bloody universe and you take me to Cardiff!"

The Doctor ran a hand through his hair and smiled charmingly.

"Well, at least I took you to 2015 Cardiff. That's in your future."

"It looks the same," Donna stated dryly.

"Well," the Doctor retorted back, "I took you somewhere didn't I."

"Yeah, Cardiff," Donna responded.

"It's seven years in your future. Lots have changed."

"Like what," she asked sarcastically.

"Cloning. Human's have perfected cloning, they even clone other people, even though I disagree with that. Its just weird."

"Cloning?" Donna scrunches her nose and quirked an eyebrow.

"Yeah! They can also take two flesh samples from two different people and mix those samples together, to create a person. Its really strange but they can make a baby out of two flesh samples. I have a feeling that the technology was borrowed from alien, its seems a little advance but that's not to bad. The Human race could always use a little boost in the right direction."

"So besides the science field improving anything else majorly different?"

The Doctor quirked an eyebrow and began stroking his chin.

"New flavored ice-cream," the Doctor replied.

Donna rolled her eyes and smirked at his response before playfully punching him in the arm.

"Do you always think about your stomach?"

"No! Not all the time at least. Ice-cream just sounded good."

Donna laughed before wrapping her arm in the crook of his.

"You are such a bloke."

"Am not," the Doctor said indignantly, sticking his tongue out childishly.

"Are too and a five-year-old bloke at that," Donna concluded, grinning.

The Doctor playfully pouted before a grin broke his face.

"Ice-cream now! the parlors down that way! Allons-y!," he exclaimed, dragging Donna along with him.

Donna chuckled.

"Why are we here anyways?"

"The Old Girl needs a refueling. She runs off of vortex energy from the rift."

Donna nodded her head in understanding. A man walked by holding a book. His hair was a neatly-combed brown and he wore sun-glasses. He bumped into the Doctor and continued to walk by. The Doctor stumbled a bit from the force of the bump before straightening his tie. He glanced back over to Donna and gave a dimpled grin.

"Ice-cream than?"

Donna rolled her eyes and they begun walking to the nearby Ice-cream shop as the Doctor rambled on about the different flavors that were available to them.

* * *

The man who had bumped into the Doctor, turned around and glared at the backs of the Doctor and Donna. He pulled off his glasses, his green eyes sparkling with anticipation. A comunicator was in his ear, he closed his book.

"Got him," he said into the comunicator, "But he's not alone."

A voice ringed back.

"_I spotted the target, he is heading towards the ice-cream shop."_

"Bit of a sweet tooth, hasn't he," the man with the green eyes smirked, "Colonel Graham wants him bagged and alive. Don't make any mistakes or he'll be extremely angry."

"_How did you know he would come here?"_

"Time rift, apparently his ship runs on the time energy. Learned about it in the UNIT files. Didn't know what time period he would appear in though. We just got lucky, I guess. I was already planning on creating some type of disaster here to attract his attention. Let loose a bunch of angry aliens or something. Luckily, he made my job a whole lot easier."

"_The red-haired chick what should we do with her. Kill her?"_

"No, that's a companion. We can use her. It said in the files that the Doctor is extremely protective of the people he travels with. When ever he disobeys we could use her against him."

"_So bag both targets then?"_

"Yes, shoot the Doctor with the tranquilizer and when he collapses, grab the companion. Do you Understand?"

"_Affirmative sir, I have my team ready and we have already blocked off the roads and created a fake accident, so we won't have any bystanders interfering. We will collect the prizes."_

"Excellent," the man,with the green eyes, said. A devious grin stretched across his face. "Yep the two mil. Is definitely mine." he shoved his hands into his pocket and began walking away, whistling a happy tune. He pulled out a cellphone.

Putting his lips close to the phone, he commanded in a clear voice, "Call Colonel Graham."

The phone dialed the number and begun to ring. The man looked at his nails and sniffed.

"_Hello,"_ was the gruff voice that answered the phone.

The Man broke out into a grin.

"Grahamy, my friend, how nice to talk to you again. How have you been?"

There was a long growl at the other end.

"_Enough games Anderson!What do you want?"_

The man, now named Anderson, shifted the cell away from his ear, a sinister smile growing on his face.

"Grahamy don't be angry, I just called to give some happy news but I guess you don't want it so I guess I'll hang up," Anderson said with fake innocent.

"_What do you want to tell me?"_ the Colonel asked contempt in his voice, _"If you're playing games, I won't hold myself accountable for putting a bullet in your skull. Understood?"_

Anderson did a fake salute and in a mockingly serious voice he replied, "Sir, yes, sir."

A grunt is heard on the other end.

"Truthfully, I believe this will make your day."

There is silence on the other end.

"We found the Doctor and my team is bagging him right now."

A dry chuckle is heard on the other end.

"_Excellent. When you return you'll receive your two million."_

Anderson was about to respond but the Colonel had hung up already. Anderson shrugged his shoulders, sniffling again, he pulled out a handkerchief and blew his nose. He stuffed the 'chief away and headed in the direction of where the rest of his team laid in wait, a smile stretched across his face and his eyes filled with greed.

* * *

The Doctor and Donna had stepped out of the Ice-cream shop. The Doctor held a double scoop banana and chocolate on a waffle cone ice-cream while Donna licked happily at a mint chip with a chocolate cone. Hand in hand they walked down the streets of Cardiff, looking through shopping windows.

"Oh Spaceman, look at that," Donna Exclaimed. She stood gob-smacked in front of one of the shop windows. The Doctor approached her, taking a huge bite out of his ice-cream, he peered through. Behind the glass window was a beautiful blue dress, with a pretty frilled pattern, and white laced gloves with matching white high-heels.

"Now that is a gorgeous dress." Donna stated.

The Doctor raised an eyebrow and took another bite of his ice-cream, slurping carefully, he swallowed. He looked over at Donna and cheeky grin spread across his face.

"I wonder if it has pockets,"the Doctor responded.

Donna grinned at their shared private joke and chuckled.

"That would make the dress convenient for our line of work." she stared at the shoes and continued, "I might have to switch the high-heels for sneakers though. Running in high-heels, not fun."

The Doctor chuckled at the memory and Donna playfully smacked him in the arm.

"Don't laugh, you weren't the one who fell face first in a puddle of mud because your heel happened to get stuck in a crack."

The Doctor laughed harder.

"I know that's why its so funny."

Donna smacked him again.

"Cheeky." she tried holding back a smile but it was too difficult, his laughing was infectious.

The Doctor felt a sharp pain in the back of his neck and he yelled out in surprise. He threw his hand to the back of his neck, pulling out a small silver needle while dropping his ice-cream at the same time. He stumbled a bit before steadying Donna looked on with concern.

"Are you alright," she asked, placing a hand on his arm. The Doctor shook his head and he felt his knee go out. He collapsed to the ground, the world spinning.

"Doctor!" Donna shouted in concern. Dropping her ice-cream as well, she helped the Doctor up.

"Donna, Run!" Donna ignored his request.

"Not today, sunshine. I'm getting you out of here."

She slung his arm over her neck and begun to drag him.

"Geez, Spaceman, you weren't kidding when you said you were a lot heavier then you looked," she grunted as she dragged him. The Doctor's eyes begun rolling into the back of his head and he moaned in pain.

"Donna run. Leave me here."

Donna ignored his request.

"Let's get you back to the TARDIS. The old girl can help you," Donna explained calmly. Dragging her friend was a lot harder than she expected and she soon grew tired.

"Hey Doctor, I'm going to lean you against this wall, ok, so I can catch my breath."

Donna leaned the Doctor against the wall of the alley-way. The Doctor tipped over, moaning, he hit his head, hard against the side-walk. A loud smack echoed when his head made contact with the cement. Blood began to seep from the wound that was created.

"No no no..." Donna screeched. She held the Doctor up and pressed her hand against his wound. Orangy-red blood seeped through her fingers. He moved his head to the side and looked at her. He took a huge gulp of air and closed his eyes.

"Donna," he moaned, "Why is the world spinning." he grabbed onto her coat, trying to steady himself.

"Shush, Spaceman, its alright. Stay calm," she tried to hush him. The Doctor's grip loosened, eyes rolling backwards. He moaned one last time and collapsed into her arms.

"Spaceman,"Donna called worried. She tried to shift his weight so he could lay comfortably. She stroked the Doctor's hair before standing up quickly.

"I'm going to find help," she told him.

She stumbled towards the entrance of the alleyway, a black van with tinted windows drove up. It screeched to a stop and armed men jumped out from the back.

"Oh No," Donna gasped. She ran back over to the Doctor and tried to drag him away, but he was too heavy. Guns clicked behind her, she turned to face seven armed men, all in uniform. She grabbed a wooden plank and swung it around.

"Stay back, I'm warning you. Come near him and I'll smack you a few," She threatened.

The men did not listen to her threat, instead they pulled out a gun and shot her in the neck with three needles. Donna collapsed. The Men surrounded the Doctor and picked him up. They dragged him back to the van and put him gently inside in fear of damaging him. they went back and dragged Donna over, tossing her into the back of the truck as well, Donna slowly opened her eyes still groggy, she watched as several of the men jumped in the back and pointed their guns at them. The doors slammed shut and the van screeched off.

Anderson made his way to the back of the truck, he looked at his two captives, and a evil smirk formed on his face. He saluted his men.

"Well done men. Did you collect the ship?"

"Yes, Sir."

"Great. This plan went better than I hoped."

Anderson bent down and poked the Doctor in the cheek, he lifted the Doctors eyelids, staring into the unconscious brown eyes, before lifting the Doctor's lip and looking at his row of white teeth. Anderson grinned.

"You're ours now Doctor. Welcome home."

Donna closed her eyes, unconscious.

The van sped down the road.


	3. Chapter 2

Please Review! I will also need some experiment ideas. So if you could give me some ideas that would be amazing.

Chapter 2

Colonel Graham marched up to Anderson, his usual scowl evident on his face. Anderson leaned against one of the cells watching a nonhuman creature, it's red eyes darting back and forth and its skin changing to a dark red. It leaped from wall to wall and scaled to the top, A group of guards were trying to pull it down, but it lashed out with tiny claws, growling in anger. One of the guards pulled out a cattle prod and shoved it into the creatures back. The creature froze and fell to the ground, squirming in pain, it flashed different colors before turning a ghostly white, as it passed out. A couple scientist brought a gurney over and the guards lifted the creature and dumped it onto the gurney, The scientist strapping it in.

"Incredible isn't it? Sometimes they can behave so human but deep down they're all dangerous animals," Anderson mused, not turning to look at the Colonel. The Scientist wheeled the creature out of the cell towards one of the testing labs, Anderson watching in fascination as they left. Colonel Graham grunted in response to Anderson's statement. Anderson walked over and picked up the clipboard and flipped through the information.

"A Chamete, hmmm... says here it changes colors based on its mood," Anderson stated, "Well, isn't that fascinating. I wonder how it does..."

"Was the Time Lord's capture successful," Colonel Graham interrupted. Anderson looked up startled, he put a hand to his heart.

"Colonel, don't sneak up on me like that," Anderson stated, pretending to be frighten, "You could give someone a heart attack."

"Answer the question Anderson," The Colonel barked.

"Pushy much," Anderson retorted, "Yeah, his capture was a success. No trouble at all, though he did bump his head, had to fix up the wound, he luckily heals quickly. You might really want to check out that healing factor of his, its quite incredible."

The Colonel stiffly nodded his head.

"I have plans for it already," he responded coldly. He turned away from the now empty cell and strode down the isle, the nonhuman creatures backing into the corner of their cells, while the braver ones hissed. Anderson watched the back of the colonel before swiftly jogging after him.

"Hey wait a minute what about my money," Anderson yelled.

The Colonel froze, he turned quickly on his combat boots and marched back over to Anderson. The colonel got right into Anderson's face, Cold blue meeting greedy green. Anderson didn't back away, he stood his grounds, and the colonel lip quirked into a snarl.

"You'll get your money soon enough," the Colonel growled. He turned quickly away and marched back to his office. Anderson straightened his tie and brushed back his brown hair. He marched down the isle and towards the exit, tapping his fingers along the white washed walls.

* * *

The Doctor woke up groggy with a bright light shinning painfully into his sensitive eyes. He threw an arm over his face and let out a huge groan. Blinking his eyes a couple of times, he shifted his body, and dizzily sat up, he clutched his face as another groan escaped. He blinked his eyes one more time, trying to rid the grogginess.

Still exhausted, his brown eyes scanned the surroundings. He was in a white cell with nothing but a thin mattress on a cold metal bunk and a toilet in a corner. He looked down and noticed his brown coat was missing including his sonic screwdriver, hearing a crackle of electricity, he glanced over to the blue force-field door. He stumbled to his feet and slowly paced over to the force-field, accidentally placing his left hand on the force-field to steady himself.

"Ahhh!" he cried out, falling backwards, he hit his left elbow on the white tiled floor, full body weight crushing his already tingling arm. Crunch. He squealed out in pain and brought his arm close to his body and moaned.

"Well, that was stupid Doctor," He muttered to himself, "way to go. Touching an electric force field. What were you thinking?"

he groaned again, as pain shot up his arm. He crawled back to his knees and steadily got up. He moved back towards the entrance and glanced across the isle to the cell across from him, red hair splayed across the tile floor.

"Donna," he whispered.

He rubbed his face and slid down the left wall of his cell. He sighed and looked up at the white tiled ceiling. She didn't run. He told her to run but she didn't. Why does she always argue? He looked over at the still unconscious Donna.

"I promise you," he whispered, "I'll get you out of this."

He stood back up, gritting his teeth from the pain. His elbow already slowly mending. He glanced back over at Donna's cell, Donna was already twitching back to consciousness. Her eyes blinked open and with a loud groan, she turned over. She rubbed at her eyes and looked through the force field.

"Donna," the Doctor exclaimed, a smile spreading across his face. Donna glanced over and smiled softly, the smile dropping when she noticed her surroundings.

"Great," she complained, rubbing her eyes, "Another bloody cell."

Donna turned over and got to her knees. The Doctor grinned at her grumbling and shrugged his shoulders. He winced when pain shot up his arm again before dying down.

"What happened to you?" Donna asked concerned.

"I landed on my elbow when I was shocked by the force-field," he responded.

"Why did you touch the force-field," Donna questioned a quirk to her brow.

"I don't know. I was being daft," the Doctor grumbled back, he moved his arm a bit, "Excellent its mending."

Donna rolled her eyes and propped herself up against the wall.

"Got any genius plans in that big brain of yours," Donna asked, she looked down at her nails.

The Doctor sighed, "A few. I just need to find the right time to execute them. I promise, I'll get you out of here, even if I don't make it."

"Won't leave without you sunshine," Donna retorted.

"Donna quit arguing. If I get you out of here, you will leave me. Understand."

Donna was about to respond when a metal door slid open, banging into there slots before sliding back together. The clipped footsteps of somebody walking over echoed off the ground. The Doctor and Donna both moved closer to the force field careful of touching it. A man jumped in front of them, his hair neatly combed back and his green eyes shining with arrogance.

"Boo," he shouted, staring at the Doctor. The Doctor recognized the man as the one who had bumped into him earlier.

"Surprised you, didn't I," He stated. He laughed and walked closer to the Doctor's cell, "You recognize me don't you. Saw that spark of recognition in your eyes."

The Doctor rolled his eyes, deciding not to dignify that statement with a response.

"I just wanted to let you know that I'm the one who caught you. That I outsmarted the Doctor," he gloated, "Me a mere human of little importance." he laughed and danced around. "Isn't that just brilliant."

Humans so caught up in their own little world. The Doctor rolled his eyes and allowed the man to rant about his brilliance.

"Now I'm getting payed two million dollars for your capture, all because I thought it up."

"Oh yes absolutely brilliant. No one would of ever thought of that," the Doctor responded sarcastically, "What was your name again?"

"I never gave it," the man said a little frustrated.

"Oh, quite right. Well, if you don't mind, I would love to have the name of the man who finally captured me." the Doctor smiled innocently, "it's been quite a while since anybody came close."

The man smirked smugly, straightening his tie, he replied, "Anderson."

"Well, Ambermint, its been truly honoring knowing that someone out there was willing to waste there life plotting my kidnapping. I didn't even realize I was that important," the Doctor responded, smiling. Anderson's face dropped. Donna smiled smugly.

"Spaceman, he was offered two million dollars for your capture," Donna added.

" Oh, I am truly honored," the Doctor said with gratitude, "See Donna, I'm not just a skinny streak of nothing."

Donna chuckled and rolled her eyes.

"Thanks a lot, sunshine," Donna directed at Anderson, "You pumped up his ego. Now I'm never going to hear the end of it."

Anderson stared in shock at the two occupants, he was hoping for fear to trickle down their spines when they learned what he had accomplished instead they turned it into a big joke.

"It's Anderson," he stumbled, "Not Ambermint." Was the pathetic response he gave.

"Oh, I'm so sorry," the Doctor responded, a grin stretching across his face, "I become so forgetful at my old age. I tend to mess names up."

Anderson nodded his head before glaring at the Doctor.

"You should respect your superiors, alien. They won't take to kindly to that attitude of yours."

"What attitude," the Doctor asked innocently.

"You know exactly what I'm talking about."

The Doctor brushed his hair back, pretending to contemplate the warning. He shook his head.

"Nope," the Doctor responded, "Don't know what attitude you're talking about. I'm normally just Mr. Friendly. Isn't that right Donna?"

"Just a big huggable teddy bear," she responded sarcastically.

The Doctor smiled at Anderson. Anderson was about to reply when Donna interrupted his train of thought.

"Anderson, don't talk out loud, your lowering the IQ of the entire cell block," Donna stated irritably.

The Doctor nodded his head. "I think you should leave, Donna's getting irritable. You can come back and gloat later."

The Doctor turned from Anderson and flopped onto the hard bunk. He rested his injured arm on his chest and closed his eyes. Anderson gaped at the way he was dismissed, glaring into the cell, he stomped off. The Doctor smirked.

* * *

"Get up," a voice growled at him. The Doctor opened an eye, to the terrible sight of a man in green military fatigues, staring coldly down at him, two guards flanking his sides. The Doctor yawned and stretched, taking his time purposefully. He wasn't going to allow these idiots to scare him.

"Get up," the Man growled again, "Or you will be punished."

The Doctor rolled his eyes and jumped to his feet.

"Pushy aren't ya." the Doctor cracked his back and moved his left arm, a smile stretched across his face, "Brilliant, completely healed. Nothing like a little sleep to heal these old bones."

The response was a backhand to the face. He stumbled back to the bunk and clutched his cheek. The man lowered his hand and glared at the Doctor.

"What was that for," the Doctor complained.

"For taking your time," the man growled. The Doctor got back up and stared defiantly at the man. The man moved closer.

"Guards bring him to lab 42," the Man commanded.

"Yes, Colonel Graham."

The two guards grabbed the Doctor's arms and dragged him out of the cell. The Doctor stumbled to his feet refusing to be dragged, The Colonel marching behind him. He glanced over and caught a glimpse of one of the lab rooms, scientist were racing around a metal contraption while different colored liquids boiled in flasks. The door swung shut and the Doctor and the guards walked by. The guards stopped in front of lab 42 before opening the door, they pushed the Doctor in and followed him into the room.

A man, in a lab coat, turned to the sound of the door swinging open. A sinister smile spread across his face.

"Welcome, Pet. I have so many plans for you," the man stated, his black eyes wide with anticipation.


	4. Chapter 3

Please Review! If you can send me different experiment and training ideas that would be great! Hope you enjoy!

Chapter 3

_A man, in a lab coat, turned to the sound of the door swinging open. A sinister smile spread across his face._

"_Welcome, Pet. I have so many plans for you," the man stated, his black eyes wide with anticipation._

The Doctor was not pleased with the outcome of his situation. The guards had force him, under the mad scientist request, to strip down to his boxers, which was humiliating enough due to the guards unwillingness to turn around, Instead they decided to jeer and make vulgar comments as he stripped down.

The Doctor tried to ignore the predicament he found himself in, but that was to much to ask, thanks to his big mouth. The guards were quite pleased to use their 'shocky sticks' on him whenever he retorted back. Within the course of five minutes he was shocked six times. He seriously needed to learn to keep his mouth shut, especially in the company of prejudice men.

The guards had dragged him to the middle of the room, where a metal table sat. leather manacles were opened waiting for the next unlucky victim. Sadly, he was the next.

The lab room felt like any other laboratory. White-washed with counters on one side of the wall that held terrible, smelling chemicals and a sink. Cabinets lined the other side of the wall with an old refrigerator underneath. But the most alarming items was the little table, next to the large metal table, that held scalpels and other surgical tools and needles. The smell of antiseptics drenched the air. The Doctor closed his eyes allowing his imagination to run wild, each possible experiment growing worst.

The Doctor popped his eyes open when the guards begun to lift him onto the bed. He pushed the guards away which earned him a sharp punch to the guts. He doubled over, clutching his stomach.

The guards dumped him on the table, not to carefully, and began strapping him in. Two of the Manacles strapped his legs down, another one went over his chest, two held his arms in place, and the last went over his neck. The guards tugging them tightly, causing the Doctor to choke when one of the guards tugged on the neck piece a little to hard.

He was immobilized unable to squirm. The only thing that had the capability of shifting was his eyes. He watched as the little mad scientist danced around the lab a little skip to his movements. Oh, that's not good. The mad scientist pulled out a long syringe, with an extremely sharp needle at the end. The scientist turned to the guards.

"Shoo, go stand in the corner over there. I have business to attend too," the man said in a high pitch voice, waving the needle back and forth. The guards nodded their heads.

"Yes, Dr. Carter," they responded to the order.

They walked over to the right hand of the wall and stood at ready in case the Doctor tried to fight back. Like that was going to happen.

Dr. Carter pranced over to the Doctor's, side waving the needle dangerously close to the Doctor's face. Dr. Carter was a short man with little muscle mass, the labcoat made him look absolutely puny, his hair, unfortunately, was of little existence, and his nose, long and narrow. The Doctor concluded the nose reminded him of a carrionite's nose. Overall, he was not an attractive man. Probably never had a proper date in his life. But what worried the Doctor the most about this man was the dangerous gleam in his black eyes. The gleam of curiosity and the willingness to put the Doctor through hell to satisfy his need for knowledge. Plus the underlying message, that this man, was in fact, a sadist. Dr. Carter leaned in close to the Doctor's face, his breath tickling the Doctor's skin.

"How are you my little pet," Dr. Carter asked, "Comfortable."

The Doctor scrunched his nose and shifted his eyes away from Dr. Carter's smile, his teeth had a slight yellowish tint. Must of not brushed for a couple of days. The Doctor shifted his eyes back to Dr. Carter and he plastered a manic grin on his face.

"Extremely comfy," the Doctor exclaimed, "you know these beds could work well in a spa, you could call the place Mad Scientist Spa, lay on our hard tables and enjoy the bright lights of our artificial sun." The Doctor squinted his eyes from the light that shined down on him. Dr. Carter chuckled.

"Glad you're comfortable because its about to get a little messy."

The Doctor closed his eyes and sighed. Where did mad scientist get these lines. Do they have a get together once a month and exchange terrible retorts or maybe they were trained at Mad-Scientist-R- US. The Doctor felt cold hands prod his arms and chest, a shiver ran up his spine and he glanced up. Dr. Carter was staring at him like he was nothing but a slab of meat. Oh, this is definitely not good. He felt a sharp jab to his right arm and he involuntarily hissed.

"Oh, I'm sorry," Dr. Carter said with no sincerity in his voice, "did I hurt you."

He jabbed harder. The Doctor rolled his eyes and looked away as Dr. Carter took his blood. The man watched in fascination as the blood came out an orangy-red.

"Oh, I can't wait to see what you look like on the inside," Dr. Carter whispered, his eyes gleaming with anticipation.

The Doctor closed his eyes tightly. Damn. This is not good.

* * *

After Colonel Graham had dropped off his new specimen, he had marched back to his office. Sitting at his desk, he shuffled through some notes on his latest captive before picking up the phone. The Phone rang three times before somebody answered.

"Send Major Johnson down to my office,"the Colonel ordered gruffly.

The voice on the other end agreed quickly before hanging up. The Colonel slammed the phone down and continued looking through the notes that Anderson had given him. A sharp knock was heard.

"Enter," the Colonel growled.

The door slammed open and a sharply, dressed man walked in. his blond hair was combed back and his brown eyes cold, he saluted quickly and stood at attention.

The Colonel stood up, his eyes squinted as he scrutinized the Major that had entered. Johnson was in his mid-thirties, a muscle bound, six foot four man. He had been known to whip any new recruits into shape and the Colonel hoped he had the capability of training a mouthy, know-it-all alien.

"Johnson," he began, "I have brought you here for one reason."

Johnson did not answer, he stood at attention like any good soldier.

"To offer you a job," the Colonel concluded.

Johnson loosened up slightly and stared at the Colonel.

"Job, sir," the Major questioned.

The Colonel nodded his head, he poured two glasses of whiskey, handing one to the Major. The Major took it with gratitude, taking a small sip, his eyebrow quirked.

"Yes," the Colonel stated, taking a quick sip from his glass, "I need you to train our newest captive, a big-mouthed alien with a bad attitude. It was brought in yesterday. You would be it's handler. Punish it when it does something wrong and reward it when it follows your orders correctly. I'll let you decide the rewards and punishments. I want you to train it to kill, fight, whatever you see fit."

Johnson nodded his head and took another sip of the whiskey.

"I think I can handle it."

The Colonel smiled. "That's why I called you in."

"May I see the information on this creature?" the Major questioned.

The Colonel tossed the file over and the major scanned through it.

"It, at the moment, is going through its first testings with Dr. Carter."

Johnson nodded his head and flipped through the pages of their newest recruit.

"You'll be working with it after the scientists are finished for the day," the Colonel responded, "I want you to whip it into shape. Teach it to speak only when spoken too. Limit its vocabulary to 'yes, sir'. This will be a difficult task since it seems to enjoy listening to its own voice."

Johnson tossed the files on the table, a wicked smile stretched across his face.

"I think I'll take your job offer, Colonel Graham. I always enjoy a bit of a challenge."

The Colonel took another sip from his whiskey glass, a smirk quirking his lips.

"Excellent, You'll start tomorrow."

Johnson nodded his head, plans already racing through his mind.


	5. Chapter 4

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Chapter 4

The doors to the cell block slid open and the quick, stomping of feet echoed off the tiled floors. Two straight, faced guards marched in, dragging the Doctor between them.

Struggling a bit, the Doctor attempted to stand, but the guards swiftly drive their metal toe-capped boots into his knee, causing him to stumble and loose his footing. From first glance, a person would assume, he wasn't well off, his left eye was swollen shut, his lip was split with a small trickle of blood flowing down his chin, and a purplish bruise formed from his cheek down to the jaw line, on the left side, of his face.

But the Doctor's brown eyes shone with determination and defiance, he wasn't going to allow these people to beat him into submission, He held his head high as they marched him down to his cell.

He no longer wore his brown pinstripe suit, instead wearing prison garbs. He wore a loose brown shirt and pants, that were one size to big for his skinny frame. His bare feet skidded across the cold, white floor.

The guards halted in front of the cell, the Doctor stumbling from the sudden cease of movement. One of the guards released his arm, stepping over to a small panel, next to the cell, typing in a code. The Doctor lifted his head to watch, but the second guard smacked the back of his head hard, causing him to loose focus. With a buzz, the force-field collapsed and the guards roughly shoved the Doctor into his cell. The Doctor stumbled, falling ungracefully to his already injured knees.

"Home, sweet, home, Subject 13," the guard, with cold, gray eyes, stated.

The Doctor turned his head, just as the force-field shot back up, and the familiar zing of electricity played across the cell. The guards laughed, turning away from the Doctor.

"OI! What the hell did you do to him, you bastards?" Donna yelled at the backs of the retreating guards.

She banged her fist against the wall of her cell. The Guards ignored her and kept walking. "OI! I'm talking to you! You better come and face me, you cowards!"

The Guards sauntered out the large door at the far end, of the corridor, one twirling his cattle prod. The giant doors slammed shut and a buzz of electricity echoed down the halls. Security cameras moved back and forth, watching each captive in their cells. The Doctor gingerly stood to his feet, slightly limping to the front of the cell. He sat against the right wall, bringing his knee's up to his chest, he rested his head against his knees, and wrapped his long arms around his legs.

"Spaceman," Donna called. She bit her lips and leaned forward, gazing into the Doctor's cell across from her. She saw a bit of movement, as the Doctor shuffled about. She saw the tips of his brown hair poke out into her line of sight.

"Yeah," he answered back. She heard more movement in his cell, his bruised face popping into view. Donna gasped. He smiled reassuringly, his eyes still twinkling with hope and determination.

"I'm alright, Donna. It's not too bad," he reassured her, he wiped off the blood dribbling down his chin.

"What happened," Donna asked concerned, "What did they do to you?" Her eyes full of sympathy.

"The Guards, apparently, think I talk to much," he said in good humor, trying to lighten the mood, he lightly smiled at her and she cautiously grinned back.

"I could of told you that," she said teasingly, allowing him the opportunity to get back into his regular, happy mood.

"And to answer your question about what they did," the Doctor continued, a little more energetic then he felt, "The Scientist, I spent the last few hours or so with, basically did an overall check-up on my health. Basically, he took blood test, tissue test, lots and lots of test. He than dragged me off to get an MRI scan, CAT scan, and a couple other different x-rays. Nothing to worry about." he smiled cheerfully. He didn't want to express his concern, with Donna, about the whole situation.

After meeting Dr. Carter, he had the bad feeling that the little creep would go to extreme measures just to satisfy his curiosity, meaning the Doctor would be in a world of pain soon, unless they escaped.

"Nothing to bad," Donna asked doubtfully, her blue eyes scanning the condition the Doctor was in. besides his face being completely bruised, his right arm had a long gash from where someone had cut it with a scalpel, and the scent of burnt flesh powerfully hit her nose, "Then why can I smell burnt flesh coming from your cell."

The Doctor gazed down and sighed, his cheerful smile dropping from his face.

"Like I said Donna, I,apparently, talk to much," the Doctor said sadly. He forced his cheerful smile back on, "But Donna there's nothing to worry about, I heal quickly. But right now we need to start thinking about escaping. I already have a few plans. But when I was,_strolling about_, out there, I found that this place is extremely secured. Crazy secured, they have lasers, darts, surveillance cameras, anything you could think of. Their very paranoid about an escape."

The Doctor looked over at the moving white cameras. The camera zoomed in on him, and the lens twisting, before turning to the other occupants of the cell block. The Doctor faced Donna once more.

"I'll let you know later, when it's time to escape. Right now, there are too many cameras. Too many people watching, I don't want you to get hurt because I foolishly blabbed out a plan."

The Doctor turned away from the entrance and steadily made his way over to the bunk. He laid down on the thin mattress, closing his eyes, and sighed deeply.

"Doctor."

The Doctor popped an eye open and turned his head over to Donna. Donna was still at the front of her cell. The Doctor got up at once, shivering as bare feet touched the cold, tiled ground. He slowly paced over to the front of the cell. He peaked out, over at Donna.

"The guards called you Subject 13," Donna stated. The Doctor nodded and rubbed the back of his neck.

"That's my new name," the Doctor responded simply. He trudged back to the bunk, falling on top once more, closing his eyes. What else could he do.

"Oh," Donna softly whispered. She too, turned away from the entrance of her cell, stepping over to her bunk, she sat down, leaning her head against the back wall, escape plans running through her mind.

* * *

"Suppers here, Freaks!" a man shouted.

Wheels from a cart squeaked on the smooth, tiled floors.

The Doctor popped an eye open from the shouting. He slowly swung his legs over the side of the bed, cracking his back, he jumped up, approaching the forcefield.

A somewhat chubby man strode along the isle, pushing a huge, metal cart. The cart held a dozen metal bowls and a huge pot was centered in the middle, steam rising from the top.

There was scraping and movement, inside the other cells, as aliens, of different species, made their way,to the front. The man brought the cart to a halt in the middle of the hall. He pulled out a ladle and plopped it into the pot.

"Come on you lot, get your lazy alien asses up and have some supper. You only get one meal a day, so don't keep me waitin' or I'll leave," the man stated, his grayish black hair was tied back into a pony tail and when he spoke, a gold tooth glinted, in the light.

More aliens stumbled to the front, all staring hungrily at the man. The Doctor curiously watched as the man dipped the ladle into the large pot. What came up couldn't even be distinguished as food. The Doctor grimaced and covered his nose from the smell. The 'meal' in the pot was a gray glop, that seemed to have little character. It sluggishly dropped out of the ladle, as the man tipped it into one of the bowls. Plop. It firmly slapped into the bowl, it slightly jiggled as the man carried it to one of the cells and slid it through the door for the alien occupant. The Doctor gulped in disgust, crinkling his nose, he turned away from the jiggling gruel.

"It reminds me of Slitheen puke," he muttered to himself, "Or the Alzarius mush pits in the marshlands."

He glanced back over at the man. The man was approaching his cell, a predatory grin on his face, and a bowl of goop in his hands.

"Well, aren't you a pretty thing," the man purred, a disturbing smile crossing his face, His gold tooth reflected the light. The Doctor stared at the man and a shiver ran down his spine. Why was it always the weirdos? The Doctor's eyes ping-ponged between the man and the goop jiggling in the little metal bowl.

"Would you like some supper. Only meal of the day. Wouldn't want you to turn into a pile of bones," the Man stated with a twisted grin, "Might not be much use if that was the case."

The Doctor sighed and nodded his head. Deciding that eating the goop was better than eating nothing at all. The man licked his teeth, his tongue lingering on the gold one.

"Good, don't want that pretty face of yours to wither away from starvation." The man opened the forcefield. The Doctor glanced over at the man's hands, dirt was crammed underneath the fingernails and dirt smudges were covering the palms. Great, unsanitary goop.

"Scoot away from the entrance, darling, don't want to shock ya."

The Doctor stepped aside and cautiously stared at the man. He decided, it was probably best to keep his mouth shut around this one, no telling what the man, with the gold tooth, would do if he mouthed off.

The man looked back over at the Doctor and slid the bowl through the little slot he created in the force-field.

"Eat up," he said, "has all the nutrients you need."

The bowl halted in front of the Doctor's feet. The contents making a sloshing, bubbling sound. The force-field closed again and the man whistled as he continued to pass out bowls of food. He came to Donna's side of the isle and handed her a plate of chicken and potatoes.

"Don't need you suffering on that alien food, sweetheart. A pretty thing like you might choke."

"I might choke," the Doctor muttered as he stuck a cautious finger into the bowl.

Donna turned to the man standing in front of her. She held her head up high.

"I think I'll eat what they're having, suffer alongside my fellow captives."

The man laughed at her. "You are a character," he stated, "Eat your nice meal and I'll collect the bowls later."

The man grabbed his cart, he gave a quick wink over at the Doctor, and strolled out of the cell block, whistling a happy tune. The Doctor watched him leave, an eyebrow raised, before turning back to the goop. The Doctor brought a finger, lathered with the gray goop, to his mouth, and licked it. His eyes widen and he cringed.

"Blah," he exclaimed, wagging his tongue back and forth, "What is this?"

Another alien, with blue skin and long white hair, turned to him.

"Supper," she simply stated.

"More like toxic waste," he exclaimed, scrunching his nose, "Or Zygon snot."

"You should eat it," the alien continued, "they get angry if you waste food."

The Doctor sighed and took another bite, the goop wiggled in his mouth, he choked it down, gagging as the content slowly slid down his throat.

"What's your name," he asked the young blue alien, a grimace still present on his face.

The alien quietly smiled, "subject 6 or if you want to get more personal, Amarzylda."

"Amarzylda," the Doctor repeated, letting the name roll off his tongue, "Pretty name, you're a Shian from the seventh moon galaxy. The planet, Shianra, correct?"

"That is correct, Doctor," Amarzylda grinned, she took another sip from her bowl and coughed, the gray goop sliding down her chin.

"Shianra, gorgeous place," the Doctor commented, "The sky's are a soft purple, with grass the bluest of blues, and so many wild exotic creatures. And the city!" the Doctor exclaimed, "the mighty city Tutolamemphris standing so tall that it surpasses the tallest tree in the Shindrin forest. Tell me Amarzylda how did you end up here?"

The Doctor took another sip of the goop, grimacing slightly from the foul taste.

"I was exploring the universe, wanted to see everything. Sort of running away from home," Amarzylda began, her purple eyes growing misty, she pushed a strand of white hair from her face, "I crash landed on Earth, I guess, in a terrible area and these men with guns whisked me away. I was so frightened. I've been here for three years,now, unable to escape."

The Doctor nodded solemnly, he stared over at Amarzylda. She was so young, barely even twenty years old in human years.

"Ama, may I call you Ama," he asked.

Amarzylda nodded her head and wiped at her eyes.

"I promise you, I'll get you and everybody else out of here. You will see your home again."

Ama nodded and sniffled, "But I don't have a ship."

"I have one, don't worry about it."

The Doctor took another bite of the goop, cringing again, before dumping it all down his throat. He shivered as the stuff slid all the way down to his stomach.

"Yep," he coughed, "Definitely a mix of Zygon snot and toxic waste with the looks of Slitheen barf."

Ama giggled.

Donna smiled at the little confrontation, she took a bite of her chicken and potatoes, feeling incredibly guilty about being the only one with the nice meal, while the Doctor and everyone else suffered from the gray stuff, they called food. The Doctor turned to Donna, his eyes serious.

"Donna don't feel guilty. Its not your fault. Enjoy your meal and relax."

How did he always know how she felt. She took a deep breath and relaxed. She knew the Doctor was right. She glanced over at the Doctor, quirking an eyebrow.

"Doctor," she stated, "I'm curious how you know what Zygon snot taste like." A playful smile lit her face. The Doctor turned to Donna, an extremely serious look in his brown eyes.

"You just don't want to know," He responded, absently rubbing at his mouth. Donna laughed knowingly, a small smile appeared on his face and he chuckled as well.

A bang was heard, as the doors slammed open, once more. Three guards came marching in.

"Get in there," one yelled, a Groske was roughly shoved through. The guards approached the quivering Groske, cattle prods in hand.


	6. Chapter 5

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Chapter 5

_A bang was heard, as the doors slammed open, once more. Three guards came marching in. _

"_Get in there," one yelled, a Groske was roughly shoved through. The guards approached the quivering Groske, cattle prods in hand. _

"I said get moving," the first guard yelled, slamming his cattle prod, in the palm, of his hand, threateningly. The guard had curly black hair, light brown eyes, and mocha colored skin. A long scar ran from his eyelid to his chin, a snarl curved his lips and he gave a sharp kick to the Groske's gut. The Groske curled in on itself and groaned. The second guard cockily strode over to the first, his light brown hair bouncing and dark eyes holding a predatory gleam.

"Maybe it's just too stupid to know what you're saying, Benson," the second guard directed to the first, a cruel smile flickering at his lips.

"Probably right, Norris," Benson responded, "It might just need a little coercion." Benson stalked closer and the Groske quickly scooted back, its eyes wide with fear. It's back hit the third guard. It turned around and looked up, gasping, it quickly backtracked. The third guard squatted next to the Groske, his eyes were emotionless and cold. The Groske raised its hands slowly, shivering. The third guard stood up and stared down at the blue Groske. He lifted an iron-toed boot and swiftly kicked the Groske in the solar plexus. The Groske skidded across the room, hitting the back wall, moaning in pain, it clutched its stomach, and collapsed to the ground. Benson and Norris laughed manically, slapping their thighs.

"Ohoho,Wells! What a kick!" Norris shouted, "I think you got air that time. Did you see that thing fly!" Benson pocketed his cattle prod and high-fived Norris.

"That taught the freak a lesson," Benson exclaimed, patting Wells on the back, "You should be on the football team! You could get plenty of practice with these animals!"

Wells gave a small smile still glaring at the quivering Groske. A tear slid down the Groske's face and it quickly wiped it away. Norris noticed the tear immediately. He strolled over to the Groske, a cocky grin on his face, he squats down at the Groske's side, with a fake sympathetic look.

"Oh," he mocked, "Did we hurt your wittle feelings? Did we kick you too hard? I'm sorry, maybe we'll be careful next time when were practicing."

Benson cackled, wiping away tears from his eyes. Wells smiled slightly at the mocking tone. The Groske curled in on itself, cowering in front of Norris. A smile spread across Norris's face, fueled by the laughter, he began poking at the Groske with the cattle prod. The Groske groaned as electricity raced through its nerves, but it was too tired to stand. It laid on the hard, white ground excepting its fate. Norris sneered.

"What? You don't like that," he condescendingly asked, "Do you want me to stop?"

The Groske nodded its head, gritting its teeth as its body spasms from the electricity coursing through its body.

"Well, I'm not going to stop," Norris exclaimed,"You're A-class entertainment..."

"Just leave him alone," a voice interrupted. Benson stopped laughing and immediately turned towards the direction of the voice. Norris smacked the Groske one last time, before jumping to his feet. The Groske hunched over and quivered.

"Who mouthed off to me," Norris asked threateningly, his eyes searching the cells. "I want to know who opened their big mouth and ruined all my fun." He banged his cattle prod against the walls, the occupants gasped in fear, they slowly scooted to the back of their cells.

"Who spoke out of line!" Benson shouted, "Because you know the rules, speak out of line, punishment will be served!"

Norris licked his lips, brushing his hair back, he shrugged.

"No one? No one spoke," he questioned, "So I guess it was just my imagination then?"

He nodded his head arrogantly, running his tongue over his teeth. "So I guess I can return to my previous activities."

He turned on his heels and strolled towards the Groske, who was laying on the floor. The Groske glanced up at Norris, he leaned over and threw-up all over the floor and Norris's shoe. Norris grimaced in disgust and shook the greenish goop off his shoe, he glared down at the creature that huddled next to his foot.

"You disgusting creature," he spat, "look what you did to my shoes!" He lifted the Groske up by its shirt and shook it. The Groske clutched its stomach. "You are going to pay for this!" he tossed the Groske back on the floor. The Groske cried out in pain, as it painfully smacked the ground. It rolled away from Norris. Greenish-blue puke covered the white-tiled ground.

"Disgusting," Wells sneered.

"Well, if you didn't kick him in the guts, he probably wouldn't of thrown up, cause and effect," the voice condescendingly retorted. The three men turned once more towards the voice.

"Who spoke?" Norris intimidatingly shouted.

"I did," the male voice stated, "And I'm not to pleased how you're treating these aliens."

Norris gritted his teeth in anger."How dare you tell me what to do!"

"How dare you treat sentient beings this way," the voice threw back.

Norris followed the voice, Benson close behind him. Wells tossed the Groske over his shoulder and carried it back to its cell, before chucking it in and slamming the force-field up. He sidestepped the vomit, following Norris and Benson. Norris halted at a cell, a tall alien stood at the entrance. Its brown hair messy and brown eyes shining with defiance and anger, freckles sprinkled the aliens nose giving it a boyish look. Its clothing too loose, on its skinny frame. Its jaw clenched and it stuck its chin up high. Norris gave it a sickly sweet grin, the alien narrowed its eyes. Benson wisely took a step back. Even though the creature was behind the force-field, Benson felt a sudden shiver run up his spine as he noticed the alien.

"What," Norris patronizingly asked, "You don't like the way I'm treating your little friends. You trying to play the big, tough hero."

The alien didn't respond right a way, Norris sneered. He slammed his cattle prod against the force-field threateningly attempting to intimidate the Alien. To Benson's surprise, the alien didn't even flinch or blink. It leaned closer, its nose almost touching the force-field. It stared Norris down, not even twitching. Norris took a step back feeling the anger sparking from the alien's body.

"I don't like you hurting these people," the alien spoke in a calm voice, "You are nothing but a coward hiding behind your metal stick and I don't approve of the way you're orchestrating that power."

Norris sneered at the tall, skinny alien, stepping forward in an attempt to regain control of the situation. It probably would have been easier if Norris didn't feel exposed. He felt like the alien was staring into his soul, picking through his thoughts and memories.

"Who do you think you are," he growled back, he banged the prod against the force-field again.

"I'm the Doctor," the alien responded. The alien straightened, eyes burrowing into Norris's.

"The Doctor," Norris snorted mockingly, "How threatening, I fix people and make them better," he sneered,"If I were you I'd think up a better name. No one can take a name like the Doctor seriously."

What Norris didn't notice was the collective gasps and increased chatter among the prisoners, when the name was mentioned. Benson turned his head, watching as the prisoners began exchanging stories among each other.

"The Doctor is here," one alien whispered. Another one nodded its head.

"I've heard stories about the Doctor, a great warrior."

"The Doctor destroyed the Daleks..."

"He's the oncoming storm..."

"Travels through time..."

"Protects the weak and helpless..."

Benson turned his head back to Norris. Norris was in the middle of a stare down with this Doctor. Benson listened to the chatter, each legend growing worst and worst. He turned to Wells, who was picking at his nails.

"Sounds like one dangerous alien," Benson whispered to Wells. Wells glanced up and shrugged his shoulders, a cold smile crossed his lips.

"We'll beat _it_ out of it. It'll soon be pissing its pants when it sees us."

Benson nodded his agreement, relaxing a bit, he sneered at the tall, skinny alien.

Norris blinked and shook his head, banging his cattle prod one last time against the force-field. He snarled and pointed his prod at the Doctor.

"I'm going to put you in your place, alien. You'll soon be cowering. The underground has no place for defiance."

The Doctor met his eyes with an even glare. "I really doubt that."

Norris gritted his teeth, anger flashing through his dark eyes. He punched the white wall.

"You haven't seen the last of me, alien."

The Doctor quirked his eyebrow, a playful smirk twitching at the corner of his lips. "Did you get that line from a cheesy movie."

Norris dangerously glared, he turned on his steel boots and marched out of the room. Sidestepping the vomit, he looked over his shoulders at the other two guards.

"Call the Damn Janitor!" he yelled irritably, "I want this bloody mess cleaned up!"

Benson nodded, raising his comm watch to his lips and summoning the janitor. Lowering his arm, he nodded his head at Wells in a 'come on' gesture, before marching after his enraged friend. The doors slammed as the three guards left. All the cell block occupants were quiet, not a sound was made, except for the struggled breaths of the Groske, a couple cells down. The Blue-green vomit seeped between the white cracks of the tiled floors. Donna glanced over at the Doctor, who was still standing rigidly still, his eyes narrowed on the exit door. He lifted a tense hand to his head, scratching the back of his neck. His lips were pursed tightly and his skin pale. He caught Donna's eyes and shook himself out of his irate mood, giving Donna a reassuring smile.

"Don't worry about it, Earthgirl. I'm fine." He wiggled his fingers to make a point. Donna's blue eyes narrowed, she quirked an eyebrow at the Doctor's response.

"They threatened you," she stated dryly, "That man, Norris, He said he was going to break you. Make you cower in fear."

Fear clouded her eyes. She couldn't bare the thought of the Doctor suffering, for the Guards own pleasure.

"Donna, I've been threatened before and have dealt with a lot worst," the Doctor stated, "These men are just cowards hiding behinds metal sticks. I am not concerned."

Donna shook her head in disagreement, her eyes burrowing into the Doctor's. The Doctor tried smiling reassuringly, at her, again. Donna frowned, brushing her red locks behind her ear.

"Cowards with metal sticks are normally the most dangerous," Donna responded wisely, "You threatened that man's ego and now he'll want payback."

The Doctor's smile dropped and he wrapped his long arms around his chest. His brown eyes shifting to the white wall, his jaw tightening stubbornly.

"I will be fine, Donna," he replied, "Nothing bad will happen to me, I'm a Time Lord for Rassilon's sake."

"Time Lord is just a title and you're not completely invincible. I just want you to be careful. This place is full of soulless monsters."

Donna ran a hand down the side of her cell wall, wishing she could hold the Doctor close. He needed the comforting and she was incapable, at the moment, of providing it. She just wanted to protect him but the electric force-field wouldn't allow it. She knew those guards would be back and she worried what they might do to her Spaceman. She feared the day the guards would arrive again, ready for revenge. She would be stuck in her cell, watching her best friend get abused and humiliated, too helpless to stop them. She shivered at the thought and pushed it from her mind. She glanced back at the Doctor.

"Just be careful, Spaceman," she repeated.

The Doctor nodded his head, turning away from her. He laid down on the hard bunk, thoughts racing through his mind.

* * *

A cheerful whistle echoed down the cell block hall and the steady rolling of wheels, squeaked on the floor. A man, pushing a Janitor's cart, stopped in the middle of the hall. He pulled out a mop and leaned it against the cart.

"Wow!" he exclaimed, pushing his glasses up his nose, "This is a big mess!" the man stared at the green-blue vomit that covered the floor, a cheerful smile evident on his face. The man was stout, his dark, brown hair thinning, and he wore a beanie on top of his head. He wore the traditional blue janitor suit. The man looked to be in his early 40's. He turned to look at the cell block occupants and cheerfully waved his hand.

"Hello, everybody. How are you doing today," he asked happily.

No one answered his question and he shrugged his shoulders. He picked up the mop and begun cleaning up the vomit.

"I guess everyone is shy today," he assumed happily. The man begun to whistle once more.

The Doctor snapped open an eye when he heard the whistling and shouting. His face was fully healed, not a bruise in sight. He only slept for about fifteen minutes or so but that's all it took for the remaining bruises to disappear. The Doctor leaped to his feet and stretched his aching arms, he sauntered over to the entrance of his cell, curiosity driving him. What met his sight made the Doctor smile. A short man, happily mopping the vomit. He wasn't grumbling or swearing, just extremely content whistling a random tune. Everyone else was silent in the room, ignoring the cheerful man.

"Hullo there," the Doctor exclaimed, "how are you doing?"

The man jumped a foot in the air, turning around quickly, eyes wide. He spotted the Doctor waving and waved back, a huge smile stretching across his face.

"I'm mopping," he answered enthusiastically, "What are you doing?"

"Oh, just hanging around," the Doctor responded, his eyes twinkling with amusement,"relaxing."

The man smiled at him and nodded his head.

"I've got to finish mopping," he said, "just keep relaxing and I'll talk to you soon."

The Doctor nodded amused and the man went back to mopping up the vomit. Suddenly, the man stood up straight and turned quickly to the Doctor. He smacked his head.

"Oh, I am so rude," the Man stated, "I forgot to give you my name. Momma always said it was polite to introduce yourself."

The Doctor grinned. "I guess it would be polite to learn names."

"Of course it is," the man said indignantly, he smiled widely, "I'm Bobby. Bobby Mills. I clean up things."

The Doctor's eyes sparkled with mirth, he lifted his hand and waved once more, "Hi Bobby, I'm the Doctor. I fix... stuff...I guess."

Bobby grinned at the Doctor, before turning back to his work.

"I will talk to you soon Doctor, but right now I need to clean this mess."

The Doctor nodded his head, thoughts and plans racing through his mind. If he could get Bobby to help him with the escape, maybe he could use materials to build a tool that can alter the surveillance cameras, getting everyone, here, out. The Doctor leaned his head against the wall, already putting together an escape plan.

The whistling ended and Bobby put his mop back into the cart. He pulled a white towel out, got to his knees, and dried the floor. He jumped up, brushing his hands together, and tossing the towel back into the cart. He cheerfully turned on his brown boots and skipped over to the Doctor, grinning. The Doctor smiled back.

"Hullo again," he hollered.

The Doctor lifted his head and winked kindly.

"Hullo, finished I assume."

Bobby nodded his head and pushed his glasses back up his nose.

"Do you know how to do origami's," Bobby blurted out. The Doctor lifted a curious eyebrow.

"Yeah, why?"

"Because my uncle knows how to make origami's. He can make a crane! So I was wondering if you knew how to do it too. Can you make me something," Bobby quickly asked.

The Doctor nodded his head. "Yeah, I can make you something. Do you have paper?"

Bobby ran over to his janitor cart and pulled out some paper, he raced back over to the Doctor's cell, holding out a pile of colorful paper.

"What paper do you want me to use," the Doctor asked kindly. Bobby looked up and rubbed his chin, he sighed.

"The blue. Blue's my favorite color," he exclaimed. He pushed the blue paper underneath the force field. There was a slight crack between the ground and force field that the Doctor did not notice before. The Doctor smiled and picked up the paper, that was slipped into his cell.

"Mine too," he responded to Bobby's statement, "My ship is even blue. What origami animal do you want?"

Bobby's eyes widened at the revelation. "You like blue too," he shouted, " that's so cool! Oh, and I want a crane!"

"Of course," the Doctor stated good naturally, he begun folding the blue paper into the shape of a crane and Bobby stared in wonder.

"You're really good at that," he blurted. The Doctor smiled and carefully folded the paper again. Bobby quirked an eyebrow. "Have you been to different planets? Just wondering since you're alien and all."

The Doctor laughed and nodded his head. "Yep, I've been to different planets. Big, beautiful ones. I've taken my friend Donna," the Doctor quirked his head in Donna's direction, before continuing, "All over. She's human and my best friend."

Bobby stared widely. "That's so cool. Can you take me somewhere one day?" Bobby asked innocently.

The Doctor smiled. "Of course. I would love to show you the universe." Bobby smiled at the promise, clapping his hands in excitement. The Doctor folded the last bit of paper for the crane and slipped it under the forcefield. Bobby grasped the crane and twirled it between his fingers, pushing his glasses up his nose, he grinned at the Doctor.

"Thank you! I wish I could make a crane."

"I can teach you," the Doctor offered. Bobby bobbed his head.

"I would love that!" he glanced over at the Doctor and blurted out, "I like you! Will you be my new friend."

The Doctor cracked a smile at the happy man and chuckled lightly."Of course, Bobby Mills. I would love to be your friend."

"That's great! I don't have a lot of friends. But I'm glad you want to be my friend." he glanced around the room, at all the other aliens, he shouted, "Hey, everybody! I've got a new friend! He made me a crane!"

The room stayed silent and Bobby frowned and shrugged. "Guess everyone's just tired." The Doctor nodded his head in understanding.

"Guess so," he muttered. Donna smiled, she had been listening to the whole confrontation between Bobby and the Doctor. She found it endearing. Leave it to Spaceman to make new friends in any situation. Bobby's smile went back to its rightful place on his face. He jumped up and looked at his watch.

"I've got to get going, I'll see you later," Bobby shouted, and was about to turn away.

"Wait, Bobby. Can I ask you a question real quick,"the Doctor asked. Bobby fell to his knees next to the Doctor's cell. The Doctor crouched down next to Bobby and moved closer to the entrance.

"Hey, Bobby," he whispered, "as a friend, can you tell me if you collect the trash, like old wires and bulb and electronics."

Bobby nodded his head innocently. "Yeah I do. All the time. Why?"

"I was wondering if you visit again, can you bring me that stuff. Like I said before, I like to fix things and I'm thinking I could probably fix whatever you bring me," the Doctor explained.

Bobby smiled. "Of course I can Doctor. Next time I visit I'll drop off some of the broken electronics."

"Thank you Bobby, I would appreciate that."

Booby jumped back to his feet and walked back to his cart, he turned to the Doctor, and waved. "Goodbye Doctor! Nice talking to you!" He opened the sliding doors and wheeled the cart out, whistling a happy tune, paper crane in his pocket. The Doctor smiled and glanced over at Donna, giving her a wink. He strode back to his bunk and leaned against the wall, plans racing through his head. Closing his eyes, he drifted to a light slumber, building his strength for the next day.


	7. Chapter 6

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Chapter 6

Dr. Carter was quite pleased with the information he had gathered, from his newest specimen, subject 13. The creature was an extremely unique addition to the agency. Many of the other extra-terrestrials, in the Underground had similar biology to that of a human, except maybe slight changes in the organs or skeletal structure. But none the less they followed the normal physiology patterns of most living organisms, one heart, a pair of lungs, and so on. But not subject 13.

Dr. Carter shifted through his notes, a crooked grin on his face, his eyes gleaming with a dangerous curiosity. The notes held the data he had gained on subject 13. All the x-rays, blood test, and flesh test he had taken that first day, the creature arrived. He flipped over the sheet, hungry eyes scanning the next section.

"Oh, yes," Dr. Carter whispered, "You are a beauty aren't you."

He drummed his fingers on the desk, before picking up a pen and underlining the data he found most useful for their cause, including bits of information he wanted to study on his own free time. He leaned back in his chair and took a sip of coffee. A sharp rap sounded on his door, Dr. Carter turned his head to the knock. His eyes narrowed dangerously. A second knock was heard, Dr. Carter rolled his eyes, turning his attention back to his data.

"Come in," he coldly stated. A young woman with short, light, brown hair stepped in. she wore a white lab coat, black pants, and a light green shirt. Her round glasses were set firmly on her nose. She marched over to Dr. Carter, High heels clipping loudly on the white floor.

"I hear the Underground has collected a new specimen," She stated icily, "Why was I not informed sooner?"

Dr. Carter glanced up at the tall woman. Her apathetic feelings towards aliens made Dr. Black one of the best scientist at the underground. Her skills also granting her a permanent place in the drug testing wing of this establishment. Dr. Carter respected Black, she was a true scientist. She never allowed her emotions to get in her way.

A sickly grin twitched at his lips, he sprung from his seat. Stepping over to Dr. Black, he handed her the data, before turning, and rubbing his hands together.

"We had just received it and I was asked to perform a thorough examination on it. I was going to inform you as soon as I had all the information gathered," He explained.

His slitted black eyes focusing on the far wall, as he pulled his thoughts together, tongue slowly running along his lips. Dr. Black's eyes scanned the notes, her eyes widening slightly with each new founding. Her tongue running along her straight, white teeth, as she flipped over to the next page.

Dr. Carter crept over to Dr. Black and looked over her shoulders. His breath tickled her right ear. He wrapped a skinny arm around her waist, pulling her close, a yellow-tinted grin on his face. Dr. Black narrowed her eyes at Carter, no emotions flashing through her blue orbs.

"Incredible, isn't it," he murmured, his tongue flicked out and touched the corner of his mouth, his eyes widened with anticipation."I can't wait to slice it open."

A smirk crossed Black's face, she stepped away from Carter, before turning, and facing him. Carter put his arm back down at his side.

"I was wondering if I could borrow it at some point? Do a drug test. See what drugs affect it the most. It would be a grand scientific achievement."

Carter's eyes widened in thought. He nodded his head in agreement.

"Do what you like my dear. I was never one to pass a possible scientific finding," he stated sinisterly.

Dr. Black coldly smiled, an experiment already forming in her head. Dr. Carter stepped closer to her and he ran a cold, bony hand down her arm. Dr. Black shivered a little, stepping back.

"I am setting up an experiment later today," Dr. Carter revealed, with a predatory smile, "I am testing subject 13's lung capacity. From what I have inquired,from the data, subject 13 seems to have large lungs that can catch every oxygen molecule it inhales, making its lungs far superior to a human's, but what is fascinating about its respiratory system, is that it has a bypass respiratory system, that collects and stores oxygen as well. I want to see how it works. You are welcome to join me. Jot down some notes for your own future experiment."

Dr. Black smirked. "I would love to join you. It's always best to learn a bit about your specimen," she stated formally, "I will stop by."

She turned on her heels to leave, but Dr. Carter grabbed her arm, with his cold hand. He stroked his fingers down the side of her arm, she turned quickly around, with an impassive glare. Dr. Carter moved closer, his pointed nose touching her neck, his lips parted.

"Maybe you can join me for a few other experiments."

Dr. Black quirked in eyebrow. Dr. Carter continued to stroke her arm.

"What type of experiments," she asked coldly. Dr. Carter seized his petting, stepping back. His eyes ogling Dr. Black, a hungry glint in his eyes.

"For subject 13," he responded, with perverse glee, "The creature, as you have read, has double of almost every organ a human has one of and four of the organs a human has two of, with exception of the liver. It has two extra ribs and its body temperature is much lower than a human's. It's core temperature is sixty degrees Fahrenheit. Not to mention its healing factor, the wounds were already healing by the time I was through with it. I want to know more and I need someone to assist me."

"I do not assist, Dr. Carter," Dr. Black retorted icily.

"I know that, but I thought we could work as partners."

Dr. Carter stepped closer. "Think about all we can find," He whispered, a horrendously crooked smirk on his face. Dr. Black knitted her eyebrows, he loved when she did that. His tongue flicked out once more, gliding across his dry lips, black eyes waiting. Dr. Black nodded her head.

"I will help you," she stated, she took a step back as Carter leaned forward, "but only in the name of science." She turned on her heels and stiffly walked out of Dr. Carter's lab. Carter stood there, a sick gleam in his black orbs, his left eye twitching. He picked up a clipboard and some other materials, before heading down to lab thirty to set up his experiment.

* * *

"Ahhh." the Doctor shot up, as electricity coursed through his nerves. He fell off the bunk and landed on the hard, white floor, of his cell, groaning softly. A boot made contact with his solar plexus, air leaving his lungs.

"Wakey, wakey, sleeping beauty," a voice taunted, "time to see the Doctor." The Doctor glanced up bleary eyed, still gasping for air. He groaned in distaste, as the face became clear. Norris. Norris smiled smugly, driving a second hard kick into the Doctors stomach. The Doctor moaned again, wrapping an arm around his abused abdomen. He heard chuckling in the back, guessing Benson and Wells were there as well. His head slammed backwards, as a hard steel boot made contact with his jaw. He felt his neck snap from the force. Calloused fingers grabbed his brown hair, tugging. He was yanked to his feet, slightly wincing as a bit of hair was yanked out of his head.

"Time to get moving freak, Don't want to keep the Doc waiting." He was shoved roughly out of his cell, stumbling slightly before gaining his footing. Norris went to grab his arm, but the Doctor defiantly pulled away.

"I can walk fine, thank you very much," He retorted, "I don't need anyone leading me around." To make his point, he stood up straight, brushing a hand through his hair, and strutted down the white colorless isle. Norris snarled behind him, slamming his prod threateningly against his palm. Benson and Wells followed close behind.

"I'm surprised you came back," the Doctor stated, a smile twitching at his lips, "Considering you left so quickly yesterday. We didn't even finish our chat."

Norris sneered at the quip. "You better keep your mouth shut, animal, or I'll shut it for you."

The Doctor glanced over his shoulders, a grin stretching across his face. "I'm curious how you would manage that. I've had that threat quite a few times, but no one has accomplished shutting me up completely."

Norris glared daggers at the Doctor. "I'm different," he growled, "I have the power to shut you up."

"Heard that one too," the Doctor responded indifferently, "If you want to threaten me, think up something original. I'm tired of hearing the same bad guy claims."

The Doctor sped up his pace, but Wells stepped behind him, and violently shoved him around the corner. The Doctor stumbled. He looked over at the three bullies and rolled his eyes. Humans and their need for power. Benson grabbed his arm, pulling him to a halt. Norris walked pass a sneer still twisting his face. Bumping into the Doctor, he grind his metal boot into the Doctor's bare foot. The Doctor's eyes widened with pain, but he bit back the groan. Norris continued pass, a smile twitching at his lips, the Doctor childishly stuck his tongue out. Norris opened the lab thirty door, marching in. Benson lead the Doctor into the lab, shoving him roughly to the floor, and placing a quick kick to his side. The Doctor glanced up, panting slightly. His eyes widened. The lab was huge, with humans in lab coats racing around taking notes and checking measurements for the upcoming experiment. Dr. Carter stood in the middle of the room, a sick smile twisting his features. Wells grabbed the Doctor by the shirt, hoisting him to his feet, and dragged him forward. Wells shoved him in front of Dr. Carter. The Doctor narrowed his eyes at Dr. Carter, glaring. Dr. Carter smirked, he moved his cold hands, stroking the Doctor's face, before pulling him down too eye level.

"How are you today, My pet," Dr. Carter asked, stroking the Doctor's sideburns. A perverse grin twitching at his lips. The Doctor smiled charmingly back, pushing Dr. Carter's hand away and standing up straight.

"Never better," the Doctor responded cheerfully, "Your guards are talented alarm clocks." He eyed the guards. Norris fumed, glaring at the Doctor and the Doctor winked before turning back to Carter. Carter studied him, with a hungry smirk. The Doctor shifted, a bit, under Carter's scrutiny, feeling slightly exposed.

"Good," Dr. Carter murmured, "We shall begin the experiment."

Dr. Carter snapped his fingers,Wells and Benson grabbed the Doctor's arms. Carter walked over to a section, on the far side, of the room. A large, glass box sat in the middle. There were monitors around the box that controlled the air pressure in the glass room. A glass door was open slightly. Lab assistance came over with sensory pads and begun placing them on the Doctor's chest and down his body. The pads would send information to the computer console about his oxygen levels, including how his lungs and bypass respiratory system would send oxygen throughout his body. The Doctor took a few deep breaths preparing himself, for this unpleasant ordeal. The Guards dragged him over to the glass box and tossed him in. The door clicked shut and the Doctor turned around to stare at the scientist. He noticed a tall, brunette woman joining the group, pen and notebook in hand. Dr. Carter walked over to the monitor, he clicked a couple buttons and twisted a key. The Doctor's eyes widened, the oxygen exited the box.


	8. Chapter 7

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Chapter 7

_The Guards dragged him over to the glass box and tossed him in. the door clicked shut and the Doctor turned around to stare at the scientist. He noticed a tall, brunette woman joining the group, pen and notebook in hand. Dr. Carter walked over to the monitor, he clicked a couple buttons and twisted a key. The Doctor's eyes widened, the oxygen exited the box._

**4 hours later:**

Dr. Carter watched in fascination, subject 13 was still alive. Its vital signs were still active and its hearts was still pumping blood. For the first twenty minutes or so, in the glass room, it had stood at the glass staring at all the scientist with desperation in its brown orbs, banging its fist against the glass walls. It stomped around a bit, before pushing at the glass door, and kicking it roughly with its foot. Carter was surprised it was still active after twenty minutes of no oxygen. It pushed its hand against the glass wall one last time, before bowing its head. It slid to its knees and proceeded to curl up in a ball, closing its eyes. At first, many of the scientist thought it had blacked out from lack of oxygen, but when they looked at the readings from the computer. The sensor pads, connected to the creature, had shown that subject 13 was still quite alive and its body functions were working properly. Subject 13 had gone into some type of meditative state that had kept it alive, for the last few hours.

Dr. Carter leaned in closer to the glass box, he tapped on it but subject 13 didn't stir. Dr. Carter glanced over at Dr. Black, a predatory smirk twisting his already heinous features. He strolled over to Dr. Black. Her blue eyes were squinted, as she took notes on the alien's vital signs, her pencil quickly scribbling down each change she found. Carter sneaked up behind her, he leaned his head over her shoulder, looking at her notes. Black stiffened, glaring at Carter.

"Dr. Carter, you are distracting me from the experiment,"Dr. Black said coldly, "Will you please remove yourself."

Dr. Carter slid his tongue across his yellow-tinted teeth. He loved her apathetic, cold nature. He took a step back, his black eyes squinting as he studied her appearance. Dr. Black turned back to her work, she pushed her glasses up her nose, and placing a strand of hair behind her ear. Carter spun around, watching subject 13 once more.

"Incredible isn't it," Dr. Carter commented, "How long it can go without oxygen."

Dr. Black grunted an affirmative, her eyes still ping-ponging between the computer and her notes.

"It seems to have gone into a meditative state," she replied, "It has, for the last few hours, been slowly using up, all the oxygen it has in its lungs. From the lack of movement, its cells do not require much oxygen. I've noticed from the readings, since the oxygen in its lungs is depleting, its body is slowly switching to its respiratory bypass system. We'll see how much longer it will last, but its hearts have slowed down quite a bit, so my guess is another 20 minutes or so, before we need to pull it out."

Dr. Carter nodded his head at the analysis. He leaned closer to the glass room watching subject 13. It's body was loosening and its fingers were slightly twitching.

* * *

It hurt. Being in this room, with no oxygen, was painful. His lungs were burning, but he knew if he tried to breath, he would only lose whatever oxygen he had left, in his lungs. The Doctor was curled up in a fetal positio near the front, of the glass wall. He was hoping the scientist would show a bit of humanity, notice his suffering, and pull him out of the room. Instead, they stood their gawking while he suffered from suffocation. He felt his lungs slowly shrivel, as the last bit of oxygen was passed through his blood stream, to his hearts, and distributed to all his cells.

He squirmed a bit. Alright, time to turn on the respiratory bypass system. He switched it on and felt a new wave of energy revive him a bit. He twitched his fingers and cracked open an eye. A small smirk crossed his face. Just twenty more minutes, before his oxygen tank would run out. He frowned. Hopefully, the scientist will pull him out, of the room, once everything inside begins to malfunction. The Doctor laid on the cold ground, his thoughts running aimlessly through his head.

A shiver ran through his body. Oh, that's not good. His right heart stopped beating. He grinded his teeth, in pain. That's really not good. He felt his left heart slow down. He gasped in agony, but there was no oxygen in the room. His whole body twitched and convulsed, screaming in silent torture. His nails dug into the floor and his head moved quickly from side to side. His twitching came to an abrupt stop, as his right heart gave out. His eyes drooped close,his body, limp. Strong arms grabbed him under the armpits and dragged him out of the hellish room. He was thrown to the floor, and an oxygen mask snapped onto his face.

* * *

Dr. Carter watched as the medical technicians surrounded subject 13. It had been dragged out of the room quickly, by one of the guards, an oxygen mask immediately slammed onto its face. The technicians raced around, talking quickly, and pulling out different medical supplies, in hopes of reviving its hearts. Dr. Carter smirked sadistically. The creature had survived four hours and twenty minutes without any oxygen, exceeding humans and any other extra-terrestrial test subjects they used, abilities. Carter shuffled over to the medical technicians, he looked over their shoulder. Subject 13 was limp, its brown hair drooping, and its brown eyes closed to the world. Its skin was extremely pale, which emphasized the many freckles on its face. The technicians pulled out a defibrillator.

"Alright," a technician states,"on the count of three, we're going to send an electrical current through the hearts. One, two, three..."

The electricity raced through subject 13's body. The creature convulsed from the sudden dose of electrical energy. The technician pulled the defibrillator away, before repeating the process several more times. The technician sitting near the monitor, studied the vital signs. A slow and steady beep came from the monitor.

"The left heart is beating again," the first technician announced. The other technicians applauded,for their success, congratulating, and patting each other on the back. A second beep came from the monitor, low and steady, but growing stronger.

"The right heart is beating. Subject 13 is stable." Dr. Carter stepped closer to the creature laying on the floor, he looked down at it, before squatting, running his fingers through its hair, a twisted grin forming. The creature's big, brown eyes fluttered open, its eyes glassy. It blinked a couple of times, before stretching out its muscles and surveying the group of people around it. Its chest rising and falling slowly. It groaned a bit.

* * *

His eyes met Carter's and the Doctor immediately scooted back a bit. He pushed the hand, that was stroking his hair, away and pulled off the oxygen mask, taking several deep breaths. He glanced up, noticing Carter's curious, predatory gaze. He shook his head and plastered a wide smile on his face. He wasn't going to allow these people to intimidate him. He glanced at the group that surrounded him, feeling slightly trapped.

"Hello," he stated, waving his hand awkwardly.

Dr. Carter inspected him, making the Doctor squirm slightly. He never enjoyed this type of attention, it always made him feel vulnerable. Carter grabbed his face and moved it from side to side. The Doctor knocked Carter's hand away.

"OI, Hands," he exclaimed, "Don't touch my face. Are you obsessed with faces or something? Because this is the fourth time you have stroked my face or hair, in the last few hours and it's weird. So, just don't."

Dr. Carter glared darkly and snapped his fingers. Electricity shot through the Doctor's already abused body. He fell to the ground, twitching. He took several slow painful breaths, crawling to his knees. He met Dr. Carter's eyes once more. Carter's sadistic smile growing larger.

"How are you feeling, subject 13?" Dr. Carter asked. The Doctor glared at the man.

"I would, probably, feel a lot better if you didn't suffocate me," he responded icily. These people were really frustrating him. They were all sadistic and twisted, with no concern for peoples well being. Dr. Carter ignored his comment and continued his evaluation.

"Incredible," he stated, he stood up, looking over at the other scientists. "It seems subject 13 has made a full recovery, after this ordeal. It is obviously coherent and able to have a conversation without feeling fatigue. It's body functions are stable." Dr. Carter gave a wide grin, the Doctor rolled his eyes and looked away. "Ladies and gentlemen, I believe our experiment was a success." The group of scientists and technicians applauded and Dr. Carter glanced down at the Doctor. "Guards take subject 13 back to its cell. Allow it a couple hours of rest, before taking it to the Major, for training." Norris and Benson stepped forward and lifted the Doctor to his feet. Dr. Carter turned away as the Doctor was lead out of the room and back to his cell.

* * *

In his office, Colonel Graham sat, at his desk. He held a syringe, with a long needle, in his hand. He brought the needle to his arm and slowly begin to squeeze the clear content into his bloodstream. He gasped, pulling the needle out, and running his tongue over his cracked lips. Beads of sweat ran down his face. He capped the needle, opening the drawer to his desk, and placing the needle inside. He sat up straight and turned back to his paperwork, a smile tugging at his lips. His cold eyes scanned the information, on the paperwork.


	9. Chapter 8

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Chapter 8

Donna paced her cell. She had heard the loud bangs and yelling, around five hours ago, and knew it was her spaceman in trouble. She had popped an eye open and seen the three men, from yesterday, drag him away to who knows where. Donna glanced out her cell concerned. She had been waiting for a long time and he still hadn't brought him back.

She had shouted at a few of the guards, that had entered the cell block, throughout the day, demanding them to tell her where the Doctor was. They ignored her, collecting the next helpless alien, and dragging it to one of the labs. That really made Donna furious.

These people had no respect for living sentient lifeforms. The way they were treating these people was horrifying, like they were animals or less than animals, all because they were from a different planet.

She had never felt so disappointed in the human race before and she was surprised that the Doctor didn't feel disgusted or hate for her race already.

She slid down the white, tiled wall of her cell, burrowing her head into her lap. She felt disgusted and she wouldn't blame the Doctor one bit, if he decided to ditch this little blue and green planet and never protect it again. Her ears perked, as she heard a loud bang as the large doors slid open. Donna lifted her head, frustrated tears streaming down her cheeks. She wiped at her eyes and slowly got to her feet.

* * *

"Move, Freak," Norris yelled. He shoved the Doctor through the door. The Doctor glared, stumbling a bit, before walking at his own pace. Norris snarled in frustration and hate. The Doctor turned his head to the intolerable man.

"I might move faster if you ask nicely," he stated with a cheeky grin. The Doctor looked straight ahead, listening to Norris grumble about stupid aliens with bad attitudes. He gasped, as an electric current ran through his nerves. The Doctor dropped to the floor from the sudden shock, before scrambling back to his feet, and swiveling his head quickly around, to the nasty chuckles behind him.

"Well, that wasn't very nice," he exclaimed at the three men.

"That's what happens when you don't follow direct orders, alien," Norris snarled, a cocky grin twisting his features. He waved his cattle prod in front of the Doctor intimidatingly. The Doctor stared, at Norris, before glancing back at the prod, he shrugged his shoulders.

"I've had worst," he stated. He turned around and continued his walk down the hall.

"I've been electrocuted several times before," he said conversationally, adding," Not counting here of course. But one time I was holding a kite for, my good friend, Ben and it was raining terribly. I was soaking wet with rope burns from the kite."

"Why the hell were you flying a kite in a rainstorm," Benson asked mockingly, though he was slightly curious.

The Doctor smiled at the hint of curiosity he received, from Benson, continuing his story, "Because,my friend, Ben Franklin wanted to conduct an experiment using electricity and creating an electrical charge. Unfortunately he handed me the kite and when lightning stroke, I was electrocuted. Hurt bad too. Advise, never fly a kite in a lightening storm. Not a brilliant idea."

"Wait, you said Benjamin Franklin," Wells stated, "_The _Benjamin Franklin, founding father of the United States."

"The one and only," the Doctor stated cheerfully, "One of my good friends too. He beat me at chess a few times though." The Doctor scrunched his eyebrows and sighed. "I swear he was cheating, but then again he was quite an excellent chess player and a brilliant man."

Norris scoffed at the Doctor's rambling, turning to his friends, "It's lying guys. It has never met Benjamin Franklin in its life."

"Oh, I may lie a bit," the Doctor admitted, "but this story is a hundred percent truth. Don't make comments about things you don't really know. It makes you look more like an idiot than you already are."

Norris growled at the insult, raising his cattle prod, he smacked it hard against the Doctor's back. The Doctor stumbled to the ground. Norris proceeded in beating the Doctor with the prod, over and over again.

"YOU DO NOT" _smack _"SPEAK TO ME IN THAT TONE!" _Smack._

"I AM YOUR SUPERIOR!" _SMACK._

"AND I DESERVE RESPECT FROM YOU LOUSY ALIENS!" _SMACK, CRACK, SMACK_.

The Doctor curled in on himself. He did not moan or groan from the pain. Just took the beating. Each blow more painful. Welts formed all over his back, as each hit became more vicious than the next. Norris breathed heavily with anger, only seeing red. All he knew was that he wanted to kill the stupid alien in front of him. Beat it to a bloody pulp. A hand grabbed his wrist, holding the cattle prod. He looked over and noticed Benson.

"Norris, calm down. You can't kill it or our superiors will be furious and who knows what they'll do," Benson reasoned, he looked down at the bloodied alien, sneering. "Don't let the thing get to you."

The Doctor uncurled and looked up at the three men, if that's what you could call them. He glared. His back feeling stiff and sore. Norris scowled at him, with hate filled eyes.

"You will respect me," he ordered. Still griping the cattle prod, tightly, in his hand.

The Doctor frowned back, but not out of hate or anger. His frown was of disappointment and defiance.

"You have not earned my respect," he stated simply. He stood to his feet and stretched his aching muscles. Norris lunged at him, but he stepped back. He could hear Donna shouting in her cell, calling the men every name she could think of.

* * *

The Doctor was beaten right in front of her and Donna was shocked. She banged on the walls and shouted every nasty thing she could think of. Watching her best friend get beaten was the most devastating situation she had ever witnessed. Her Spaceman,was a proud man and watching these men try to steal his pride was horrifying.

"LEAVE HIM ALONE!" she shouted, "YOU INSECURE RACIST PLONKER!"

She watched the Doctor stand to his feet, she could tell from his stiffness, he was in a lot of pain, but didn't want to show it. She smiled at his determination, as he told the idiots off. The Man, Norris, smacked him across the face, the Doctor didn't even bat an eye. They shoved the Doctor into his cell roughly, before scurrying off, like the rats they were. Donna scoffed in anger.

"Yeah you better bugger off, you arses!" she shouted angrily, kicking her cell, she brushed a frustrated hand through the mess of red hair. Her piercing, blue eyes swarming with rage, at what she had witnessed. Norris turned around quickly, glowering at her, a sneer lifting his lips.

"Shut it, you ginge. Or I'll teach you a lesson next," he threatened, pulling out his cattle prod.

The Doctor immediately jumped to her rescue. "Leave her alone you coward! Don't take your frustration out on an innocent woman! Take it out on me!"

Norris glared at the Doctor, he ran a finger across his neck and pointed at the Doctor, before turning and following his friends,stiffly, out. The door slammed shut. The Doctor glared at the door, before plopping onto his bunk, groaning.

"Are you alright,"Donna asked, though she could slap herself, for asking such a stupid question. She just saw her best friend get beaten, of course he wasn't alright. The Doctor glanced over at Donna, nodding his head.

"Fine," he stated, "just a little sore. Your right I shouldn't poke at the guards insecurities. Not the brightest thing I've ever done." The Doctor gave a small smile of reassurance. Donna nodded her head, a frown still placed on her face.

"I'm sorry I couldn't help you," she choked out, she felt the tears brimming at her eyes and she buried her face into her hands, "I'm such an awful companion and friend. I couldn't protect you, I tried but they ignored me. How can you handle me. I'm useless." She sobbed. The Doctor stared sympathetically. This place was taking its toll on everyone. He wanted to hug her and tell her everything was going to be ok, but he just didn't know at this point, plus he couldn't reach her. Hopefully, Bobby would follow through with the plans. It would make escaping a lot easier.

"Shush, Donna," he soothed, "I'm ok and none of this is your fault. I was egging them on and you warned me not too. So, don't worry."

Donna sniffled and rubbed at her eyes. "I'm an awful friend though. I wouldn't blame you if you decided to dump me back at home."

"Donna," he sighed, "I'm not going to dump you. Your my best friend and you've done nothing wrong. Don't blame yourself for a situation, you couldn't control. We're both still alive and that's all that matters."

Donna nodded her head miserably and sniffled. Her nose and eyes were red from the sobbing. She felt like a mess. She chuckled bitterly. She glanced back at the Doctor, before staring down at her feet.

"They took you away earlier today," she stated, "Why?"

The Doctor waved a hand in dismissal, "More test. Nothing to worry about." He stared at his hands, crossed, in his lap and sighed.

"What type of test," Donna ventured, her voice strained. She knew, from his tone, he was trying to hide something from her. The Doctor mumbled under his breath, before sighing.

"They wanted to test out my lungs, how long I could hold my breath," he replied, not willing to look her in the eyes and see the horror and pity.

"Did they drown you?"

The Doctor shook his head, and scratched the back of his neck, messing his brown hair even more.

"No, more like stick me in a room with no oxygen."

Donna nodded her head, her bottom lip wobbling, she swiped her hand across her eyes once more.

"I'm sorry," she stated miserably, "for everything."

"Don't be sorry. You didn't do anything wrong. There was no way to prevent the incident."

The Doctor laid down on the bunk, his back facing the wall.

"But I need a bit of rest," he continued, "I have training in a couple of hours and I need to heal these wounds."

He closed his eyes, trying to relax and enter a quick healing coma.

"Doctor." he popped an eye open. He hummed in response.

"Bobby came today," she said, "He cleaned up your cell, while he was here. We had a nice chat. He said he'll visit you later. He cleaned under your bunk." Donna nodded her head over to the bunk and raised an eyebrow. The Doctor's eyes widened.

"Oh." he bent over and looked under his bunk. A pile of wires and broken electronics were stacked neatly underneath. The Doctor smiled at the pile of junk before rolling back onto the bed. "Good ol' Bobby." He closed his eyes and entered a healing coma. Already feeling the welts heal and disappear.

* * *

Next chapter will be training with Major Johnson. I had to split the events into two chapters, because they wouldn't fit together neatly. Besides, I needed this chapter for a bit of Donna and Doctor angst. Hope you enjoyed and please review!


	10. Chapter 9

Sorry for the wait, this chapter took a while to write. A lot of stuff happens to the Doctor. I hope you enjoy! Please review! I love reviews!

Chapter 9

The doors slammed shut, and the quick clips of feet were heard on the tiled floor. The Doctor popped an eye open and sighed. He glanced out of the opening, in his cell, to notice a couple of guards, walking down the cell block hall. The Doctor rubbed his arm over his eyes, sighing heavily again. Apparently, his two hours were up.

He sat up, just as his cell force-field fizzed out and two tall men stood in front of them. One of the men summoned him over, while the other stood behind and watched, waiting for any struggle. The Doctor jumped to his feet, stretching his sore muscles. He was still slightly sore, but the two hour healing coma had fixed many of the welts and bruises, except for the occasional scar.

The Doctor slowly stepped over to the guards. Each step, his back muscles twinged and pain laced through his aching body. Sleeping on a hard bunk and getting beaten a few times a day had taken its toll, but he had only been here a few days, so he wasn't going to let this situation bother him. He and Donna will be out of here in no time. The Guards shoved him out of cell and he stumbled slightly, before one of the guards grabbed his arm.

"OI! Where are you taking him!" Donna shouted from her cell. "You better not hurt him!" The Doctor smirked at her threatening tone and the loud stomping and banging that racketed from her cell. The Guards ignored her shouting and continued their progress down the hall, with the Doctor in tow. The Doctor glanced up at his guards, who marched in stoic silence, staring straight ahead. The Doctor raised an eyebrow, a cheeky smile crossing his face.

"Nice night for a stroll," he said playfully, he looked straight ahead, "What have you two boys been up too lately? Anything fun?" The guards did not answer.

The Doctor sighed and continued his random ramble, "It was nice of you to stop by and escort me to my next activity, it gets kind of lonely down these halls. You have to watch out for dangerous predators and boy, do I know there are quite a few here..." the Doctor paused for a second, surveying the two men that escorted him to the training arena.

They were both tall, like most of the guards here. Strongly built with an air of intimidation. The Doctor's eyebrows lifted quizzically. "You know, you two look like all the other guards. Same built, same personality...well, not exactly same personality but still, some are a lot nastier then others, and are required to hate aliens. Does your employers send out a job description for these character traits because you're all exactly alike and its weird." the Doctor's eyes widen, as a thought crossed his mind."Oh, unless your robots! I would believe it to, if that was the case. What do you say?" he glanced up at the guards that were leading him. They did not reply, didn't even blink, they just continued their simple march.

The Doctor grinned widely. "You guys are like the queen's royal guards, completely stoic. Do you two ever smile or is it because you're with me. I don't mind a bit of talking and if you're worried about getting in trouble, my lips are sealed. But of you don't want to talk, that's ok. I'll just entertain you with my charming personality. I have plenty of stories...AHHH!"

The Doctor fell to the floor, twitching. As electricity raced through his nerves, like a thousand, tiny needles. His Body trembled and beads of sweat rolled down the Doctor's face, he breathed heavily, glancing up at the guards. He rolled onto his stomach and steadily getting up onto his knees. The guard on his left grabbed his loose shirt and yanked him up to his feet. The Doctor groaned slightly from the sudden movement, as black spots danced in front of his eyes. He shook his head, trying to clear the dizziness. The guards pushed him and he stumbled forward, the march continued.

"I get it," the Doctor announced, "Prisoners aren't allowed to speak. Which I find quite rude because what if I had something extremely important to say. Like if I shout 'fire' and a fire is spreading throughout this secret agency. I might just save everyone's life at some point."

_Smack, _The Doctor tripped a bit, as a rock-hard hand hit the back of his head. The Doctor clutched his injured head, squeezing his eyes shut, before slightly opening his eyes to stare at his guards. He stood up straight once more.

"Ok,"he stated, sarcasm dripping from his tone, "My mouth is zipped shut." He makes the zipping motion with his hand, turning away from the guards. The rest of the march, was met with silence.

* * *

Major Johnson stood on a mat, in a huge technically, advanced gym. His hands were crossed behind his back, and his chin held high. His blonde hair was pushed to the side, and his light, brown eyes sparkled dangerously as he saw the two guards approach him, with the creature in tow.

The creature, looked like a handsome, young man between the ages of late 20's to mid 30's. It was tall, probably standing at six feet, but extremely skinny. It's shirt hanging off its thin shoulders and pants to large to, possibly, fit snugly around its waist. It's dark, brown hair stuck out in every direction, giving it a naughty schoolboy look, the freckles dotting its face didn't help reduce that image either.

But what really concerned the major, about this alien was its eyes. By staring into the eyes, of subject 13, he could immediately tell the creature wasn't going to be easily trained. It's wide brown eyes appeared young, but Johnson immediately sensed the old man behind the young face. Those eyes held the universe and all of time and it was terrifying. But Johnson had a job, training this creature and he wasn't going to allow some freaky alien eyes to scare him away, from this opportunity.

Johnson sensed the creature was stubborn. Its jaws were set tightly expressing its dislike for the situation and it held its head high, staring the major down, with a defiant grin. The guards pushed it forward and it fell onto its knees in front of Johnson. It glanced up, before gracefully getting to its feet, and staring back at the Major. Johnson was at least three to four inches taller than the alien in front of him. He bent forward getting right into the aliens face, locking eyes. The creature didn't even flinch, from the close contact, it stood steady, no fear in its expression. The Major gave a small smirk, his eyes squinted. Well, he was about to fix that. A larger grin spread across the alien's face, its way of showing the Major it wasn't afraid.

"Hello," subject 13 said, "I'm the Doctor." It glanced around the room taking in every detail.

* * *

The man, the Doctor stood in front of,glared menacingly down at him. The Doctor had to raise his head slightly to meet eye to eye with the blonde haired tank. He had introduced himself and charmingly smiled, before looking around the room he was shoved into. The room was huge. Mats were laid across the floor, with treadmills and other exercising equipment on the sides, a boxing ring sat to the left side of the gym. There was a door at the far end, that was closed. He looked back at the man in front of him. The man's light, brown eyes were cold, expressing an apathetic and, possibly, cruel nature.

"Just like everyone else in this place,"the Doctor muttered to himself.

_Smack! _The Doctor stumbled back as the man backhanded him across the face. The Doctor grasped his cheek in irritation, a hand shaped bruise already forming. The man had the strength of a tank as well. The Doctor glared at the man in front of him.

"Oi!" he exclaimed, "That was rude! Didn't even give me a warning. I didn't even do anything annoying this time. I didn't deserve a slap across the face!" The Doctor huffed in frustration. The Man looked down on the Doctor, his nostrils flaring.

"I am Major Johnson," the man,or Major Johnson, stated coolly, "I am your trainer. Whatever I order you to do, you do it. If you argue, you will be punished. I do not like disobedience and what I've witnessed from you so far, you are a rebellious, stubborn creature, who doesn't take orders well." The Major glared down at the Doctor. "I don't allow that. Is that understood."

The Doctor smirked. "Can you repeat that. I didn't quite catch it all. I'm old and most threats go through one ear and out the other."

Johnson pulled out a baton and slammed it into the Doctor's stomach, the Doctor gasped from the sudden attack, doubling over. He curled his arms around his stomach, gaping like a fish, eyes wide from the pain. Johnson pulled the baton back, slamming it against his palm threateningly. The Doctor breathed heavily and looked up with glazed pain filled eyes.

"Speak when spoken too, subject 13, or your punishments will get a lot worst," the major stated icily, a vicious smirk quirking at the corner of his mouth. "And I am an extremely creative person when it comes to punishments."

The Doctor stood up straight. He wasn't going to be intimidated by this man in military wear. He grinned cheekily. "But you did speak to me Major and I answered. I didn't break any rules."

_Slam!_ The baton made contact again with his already bruised stomach. _CRACK!_ The baton made contact with his shoulder and the Doctor fell to his knees, from the sudden force of the beating. The Doctor closed his eyes in pain, breathing heavily through his nose. He popped an eye open, glaring defiantly at the Major. He really needed to learn to keep his mouth shut, in certain situations. The Major coldly glanced down at the Doctor, who was kneeling on the floor, one arm holding his bruised stomach and the other rubbing his injured shoulder.

"The correct answer is 'Yes, Sir'."

The Doctor nodded. Johnson stared down at him expecting an answer. The Doctor swallowed heavily knowing this was going to hurt his pride, but the conversation needed to be pushed forward. He sighed heavily.

"Yes," the Doctor stated. He looked up at the Major who stood statue still, his face stone cold, except for the eyebrow quirked in expectancy. He waved the baton slightly, threateningly, and the Doctor took another gulp of air, before breathing out. "Sir." he cringed with distaste from the words that just left his mouth. Compliance. How could he cooperate with such a horrible man. He was the Doctor, for Rassilon's sake, top of the universe and he just uttered a 'yes,sir' to a human, a despicable human none the less. He felt low. Well, this was the last time he was going to comply. Hopefully.

Major Johnson smiled in triumph, he placed the baton back into its holster. He crossed his arms behind his back and circled the Doctor. The Doctor froze under the scrutinizing eyes of the Major. The only part of him that was moving, was his own brown orbs that followed every step the Major made. Johnson cleared his throat slightly, staring down at the Doctor.

"Today," he begun, "I am going to test out your speed and strength. See where you're at and where I should start your training. I will evaluate your abilities and next time we meet, I will design a course for you that will challenge your weaknesses as well as your strengths." He halted his movements for a second, waiting for any interruptions from the Doctor. The Doctor, wisely, kept his mouth shut. Johnson continued his circling, evaluating the Doctor's position. "I will test your reflexes, training you to fight and kill." the Major smirked slightly. "Which I doubt will be a problem after reading your file. Killed a lot of people haven't you."

the Doctor flinched from the mental jab. Well, that hurt. Major Johnson continued, "I will train you in the finest martial arts. You will be unbeatable. The Ultimate weapon." the Doctor rolled his eyes in annoyance. A little too late for that, buddy, I can probably take you out in a few seconds flat. Humans, think they know everything. The Doctor sighed in irritation. He just hoped this explanation of what will happen in the future, would soon end. He was getting bored. The Major ended his pacing, he glared down at the Doctor. "Do you understand?"

The Doctor glanced up and sighed heavily, he composed himself, ready to break his ego one last time. He mind as well, he was no use broken physically. The Major tapped his foot, waiting for an answer, his hand reached for the baton at his side.

The Doctor blurted out a quick, "Yes, Sir." Groaning inside. This was humiliating. He should not be bowing down to this idiot in a military, monkey suit. He was a Time Lord! But, the man said he was creative with punishments, he might hurt Donna if the Doctor argued. He wasn't going to cower, in front of Johnson, he'll still throw in a couple of jabs, but not enough to threaten Donna's safety. He glanced up at the Major, noticing the satisfied smirk. The Major cleared his throat.

"Seems you learn quickly. Good, makes my job a lot easier." He lifted the Doctor up by the arm, leading him towards the closed door at the far end. The Major pulled out a pair of keys, unlocking the door. He shoved the Doctor through.

* * *

Inside the room was something that could only be defined as a giant jungle gym. It reached all the way to the top of the ceiling, at least fifty feet tall. Platforms were lined across the room, held by chains.

They swung back and forth as nothing underneath held them still. The platforms were separated at least five to ten feet apart. The platforms circled around a giant pole, reaching to the top. Ropes hung from the platforms, and vents and trap doors were inside the gym walls. Large ropes that took the form of a bridge, hung twenty to thirty feet in the air, there was no bottom, so you had to walk across it like a tightrope.

In the middle of the large tower, was a larger platform with rails, again it swayed back and forth, a door was at one end of the platform. At the very top a green button sat, ready to be pushed.

The Doctor had a bad feeling about this training exercise, it looked easy enough, but he knew that the ominous doors and vents were there to make his little climb difficult. Great.

Major Johnson glanced over at the Doctor, a satisfied smirk on his face. He cleared his throat, before speaking in a clear voice. "This gym, will help me evaluate your skills. Your task, that you have to complete, is to reach the top and push the green button. You must reach the top in exactly one hour. But there will be traps along the way, you must dodge them or fight them off. Operatives will attack you. You will have to fight them off to the best of your abilities. If you run, they will chase you, keeping you away from the green button. You must disarm them. If you don't you will be punished. Do you understand?"

The Doctor nodded his head. "Yes,sir. Except I have a quick question." The Major glared menacingly at the Doctor, irritated that he was stalling.

"Are the operatives people or robots?" the Doctor glanced at the Major, expecting an answer. He noticed Johnson's fingers twitching near his baton holster and the Doctor stiffened ready for a blow. The blow never came.

"Robots," the Major answered, "I didn't want to risk human life on your first day of training." The Doctor let out a sigh of relief. He nodded his head once more, and did a quick mock salute.

"Well, than. Lets get this evaluation over with," the Doctor exclaimed happily, he bounced over to the start of the course, wrapping his long fingers around one of the ropes, he looked over at the Major, who had his arms crossed. The Doctor gave a dazzling smile, shouting, "Allons-y!"

Pulling himself up, onto the rope, and climbing to the top, where he jumped up onto the first wobbly platform. He backed up slightly, before running across the first platform and leaping ten feet to the second platform, landing gracefully on his feet. The Doctor gave a small laugh. This was actually fun.

"You will be exterminated," a nasally, mechanical voice spoke. The Doctor turned around to see a giant robot, stepping forward. Its metal body, flashing in the bright light, and red eyes blinking menacingly. But what concerned the Doctor the most, was the large gun in its hands, and the little razor blades protruding from its fingertips. A second one stepped out, on the Doctor's other side, with a similar promise of death. The Doctor groaned, he had spoken to soon.

"Great," he muttered under his breath, before leaping into action and kicking the first robot in the head, before swinging his right fist around and punching the second in the face. The Doctor landed on his feet gracefully, as the robots stumbled back, a predatory grin stretching across his face. The robots shook their heads and raised their guns. Flashes of laser energy bounced back and forth, the Doctor ducked and the energy destroyed the two robots. He sighed, the Major wasn't kidding when he said a few attacks. The Doctor raced away from the robot carnage, jumping from one platform to the next.

* * *

This was not fun. The Doctor ran across the platforms, jumping from one to the next, with a hoard of killer robots oh his back. He skidded to a stop, realizing the platforms had ended, on this level. A shot of electricity whizzed past his ear and he stumbled back.

"Not fun. Not fun. Not fun," the Doctor muttered to himself over and over again, as he prepared to jump, for the rope that hung from the third platform level. The platform, he stood on wobbled and groaned with protest.

The Robots approaching closer. He leaped for the rope that hung down, grabbing tightly, he pulled himself up. His muscles groaning with agony. His clothes were burnt rags, thanks to the damn robot lasers, and he had bruises all over his body from accidentally stepping on a trap door and tumbling ten feet down and cracking his head on the metal platform below. Which the fall had awoken the several angry, killer robots that were now chasing him.

The Doctor jumped up, grabbing a ring and hoisting himself up, he stumbled on the platform, just as a razor blade swung, at his head, almost decapitating him, he ducked. The razor clipping his shoulder and blood oozed down his arm. He ducked again, as the razor blade swung back down. The Doctor looked up at it. Giving him an idea. The robots were already making there way to the top. The buzzing screams of exterminate, heard from below.

Seriously, did the Major get that line from the Daleks and insert it into the robots. He most likely did. The robots made their appearance crawling onto the platform, like a hoard of army ants. Their red eyes flashing, the Doctor ducked a third time as the blade swung back and forth. The Robots crawled onto the platform, causing it to groan and wobble under the mass of weight. The Doctor growled, determined to escape the swarm of murderous robots.

"Hey, come and get me," he shouted, alerting the robots to his direction. He bent down under the swinging blade. The robots lifted their guns at the Doctor.

"YOU WILL BE EXTERMINATED!" They shouted together. They stepped forward and the Doctor crawled back a bit. Luckily, the robots weren't the brightest, of the lot, and were immediately sliced in half from the oncoming blade, their robotic pieces shattering everywhere. With a small explosion, the robots self destructed. The Doctor laughed happily about his achievement, crawling away from the swinging blade. He stood back to his feet, laughing manically. Oh, he was losing it.

A crack was heard from underneath him, he looked behind him and saw the platforms begin to break apart and tumble thirty feet to the ground. The Doctor turned around and begun running as fast as he could, as parts of the structure broke apart, the crack following him, he jumped to the next rope and quickly climbed up, just in time, as the whole third floor platform, collapsed.

He breathed a sigh of relief, just as flames shot through one of the vents straight at him. Singeing his clothes and hair. The Doctor quickly climbed up, as the fire made contact, with his bare feet. The Doctor gritted his teeth in pain, grunting slightly. He smelled like burnt flesh and probably looked a whole lot worst. The Doctor rolled onto the fourth platform. Breathing heavily. This was a lot harder then he expected.

He heard a snap, just as a lead weight fell towards his face, he rolled out of the way quickly, and the weight made contact with the platform. Shaking it dangerously, one chain snapped, causing the whole platform to slant. The Doctor scrambled to his feet, sprinting along the slowly tipping platform, and jumping, as fast as he could, to the next one. He missed it. He shot out a hand, grasping the edge, with his sore, raw hands grunting as he pulled himself up. His muscles screaming in pain from the strain.

He rolled onto the new platform, gasping for breath, before shooting off, avoiding another catastrophe. He skidded to a stop, almost falling over the edge. There wasn't a new platform for him to jump onto, instead two giant ropes were connected from one platform to the next, twenty feet on the other side. The Doctor groaned and slowly pressed a burnt, swollen foot onto the dangerously, high rope. He quickly looked down, quickly regretting his peak. As the world seemed to spin dangerously from the height he was at.

"Oh," he muttered, "That is really, terribly high." He took a giant gulp of air, placing his second injured foot onto the rope, losing his balance slightly. He threw his arms out, balancing his weight, as he took another cautious step.

"Ten more minutes, before the goal time is up," he stated to himself, scoffing sarcastically, "No pressure at all."

he slowly made his way across, breathing slowly. He slightly dipped to one side, before quickly straitening himself up. Quickly making his way across the rope. The rope digging into his sore, mangled feet.

The Doctor hopped to the other side, just as a laser shot over his head, he fell to his knees and the platform wobbled from the weight of a metal foot landing on it. The Doctor looked up to see a robot pointing a gun at his head. The Doctor stumbled to his feet, preparing to fight. The robot shot a second laser and the Doctor slid out of the way. The platform wiggling dangerously. The Doctor ran forward towards the robot, sliding under its arms, to the other side of the platform.

"Five minutes," the Doctor murmured.

The robot's head turned a one-eighty, staring at the Doctor with its red, beady eyes. Its body turning in the position, of where its head was now facing. The Doctor quickly kicked the robot in the soft spot of its knee, where the two parts of the leg connected. The robot stumbled and the Doctor quickly punched it in the throat, dislodging its head from its shoulders.

The robot waved its arms around still holding the gun, in its left hand, as it swung its right clawed hand at the Doctor. The Doctor spun out of the way, of the sharp claws, his eyes quickly scanning the robots, mechanical body. He spotted a small button on the left side, behind the robot's arm, just before it swung its right hand, smacking the Doctor hard across the face, leaving two long gashes on the Doctor's cheek.

The Doctor growled in irritation, as he leaped forward. Faster than the eyes could blink, the Doctor quickly disarmed the robot, breaking its right arm off, with sudden force and strength. He twirled quickly out of the way, as a laser grazed his ear. Before he jumped forward, quickly twisting the robots arm with the gun, yanking it off. Electric wires sparked from where the robots arm used to be. The Robot ran towards the Doctor,but the Doctor quickly turned out of the way, throwing his hand out and slamming the tiny button, on the robots left side. The robot collapsed forward, the Doctor jumping out of the way.

The Doctor turned away, tossing the robot's arm onto the ground. A snarl lifting his lips. His hair singed on the top and his clothes tattered. Black smudges covered his face and a hard glare was in his brown eyes.

"Three minutes," he announced to himself. The robot exploding behind him, a small smirk crossed the Doctor's face. He continued his sprint and jumps around the fourth level platforms, before jumping up and quickly climbing up to the fifth level. He could see the the button in the distance.

Leaping from platform to platform, the Doctor had no interruptions. He had two minutes left and he would soon be done with training, for the day and be allowed to relax back in his cell. A manic smile crossed the Doctor's face, as he saw the green button growing closer, he skipped slightly with excitement, laughing manically. Yes, he was definitely losing it.

He stopped right in front of the green button. His hand raised, ready to press it, and be over with this. His laughter growing more manic by the second.

"The green button," he exclaimed happily, insane laughter filling the gym, "I made it. I am almost done! I have beat this!" he cheered. His smile, if possible, grew wider, as he lowered his hand to press the button. But at that moment a strong electric laser, smacked him square in the stomach. With a sudden 'oof', he flew backwards, his butt skidding across the metal floor. He laid on his back, time ticking by.

"No no no no no!" he shouted childishly. He was so close. Right next to the button, he could just reach it. He sat back up, slowly getting to his feet. He looked over at the gun, on the other end, shooting sporadically.

"fifty three seconds," he groaned. Blue electric streams shooting everywhere, like tiny arrows. The Doctor stood.

_Forty seconds. _The time ticked by.

"I am not going to be punished for failing," the Doctor growled determinedly to himself. He braced himself, ready to leap into action.

_Thirty seconds._

The Doctor ran forward, electricity whizzing past his ears and over his head. He ducked, and leaped out of the way of the oncoming electric arrows. Running forward.

_Ten seconds._

The Doctor ducked, moving swiftly over to the green button.

_Nine seconds...eight...seven...six...five...four...three...two..._

He lifted his arm, just as the electrical current whizzed over his hand. Sweat dripping down the side of his face and teeth gritted in determination.

_One...zero..._

He slammed his fist onto the green button, just as the alarm for the end of the course ended. A shrilly, flashing light went off over his head. The gun shutting down. The Doctor groaned in relief, laughing hysterically. He made it. He turned onto his stomach, wincing from the spike of pain, that shot up his nerves. His clothes, basically, didn't exist anymore and his hair was so burnt, that it curled in charred, black chunks on the top. Black smudges and bruises covered his face making him unrecognizable. He groaned, exhausted.

"Are you coming down," a loud voice yelled up to him, "Because if you're not down in two minutes, you will be punished brutally for your disobedience." The major threatened.

The Doctor groaned, couldn't the man give him a break, he just ran a whole bloody course, that was hell-bent on killing him.

"If you don't answer on the count of three, you'll be running it again!"

That caught the Doctor's attention. He rolled to his stomach, getting to his knees.

"ONE!"

He stood painfully too his feet, wincing as every muscle protested against the movement. His raw, bare feet screaming in agony with every step, he took.

"TWO!"

He slowly made his way over to the edge of the platform, glancing down at the fuming Major Johnson. "What a jerk,"the Doctor mumbled to himself.

"THREE!"

The Doctor took a big gulp of air, shouting down to the Major. "Yes, sir! I'm coming down!" The Doctor turned away and slowly walked over to the rope and lowered himself down to the fourth platform.

"Two minutes," The Major barked, "Or you will be punished for your disobedience!"

The Doctor rolled his eyes in irritation. His feet touched the fourth platform and he limped towards the next rope, gritting his teeth.

"Yes, sir," he muttered sarcastically, "Anything you say, sir. I'll do your bidding, sir. Do you want me to jump through hoops, sir, or would you prefer me to get shot by killer robots." He ranted angrily to himself, as he made progress down the terribly, high, death gym.

* * *

The Doctor limped over to the stoned face Major. He came to a halt and glared at the human in front of him, an angry sneer growing on his face, before he forced it into a happy smile.

"Piece of cake," he announced sarcastically, as he swayed in front of the Major. The smell of burnt flesh and hair clogged the air.

"You look like a mess," the Major stated, cold eyes scanning the Doctor's state.

The Doctor snorted in annoyance."I wonder why," he retorted, sarcasm dripping from his lips.

The Major didn't respond to the tone, he just gave an even glare, watching the Doctor's every move.

"You did better, than I expected," the Major mused. He poked the Doctor in the shoulder, before lifting the Doctor's chin, and looking over the burnt marks down his neck, as well as the bruises and grease smudges covering his face. The Doctor's lips curled in irritation.

"What were you expecting," the Doctor asked, anger flashing through his eyes.

The Major released the Doctor's chin, folding his hands behind his back.

"Failure," he stated simply.

The Doctor couldn't keep the growl that slowly released from the back of his throat, he was really pissed. Johnson ignored the growl, just glowering coolly down at the Doctor.

"I can't punish you since you beat the course," the Major said, he glanced at the Doctor, before turning his attention away, from the angry alien. "I guess I have to reward you, since you did something right." The Doctor kept his mouth shut, not wanting to ruin the possible reward. Johnson flicked his hands over at the two guards. The guards marched over, heads held high. Johnson turned to the guards.

"Take Subject 13 to the showering room," Major Johnson ordered, "He deserves it. Also, find him fresh clothes. These rags are falling off of him." Johnson sneered at the mention of rags, before turning away from the guards and marching off.

The Guards grabbed the Doctor by the arms, dragging him to the showering room. A happy smile playing at his lips. He didn't want to say anything, in case he lost his reward. He deserved that reward too, after what he went through. He happily walked into the showering room. The door snapping shut behind him.


	11. Chapter 10

Please review! I love reviews!

Chapter 10

Donna laid on her bed, tracing the many white lines on her wall. She was so bored. The past few days, she had done nothing but sit here and worry about the Doctor's health and safety. Every time they took him away, Donna grew a little more worried about him. Yes, it had only been a few days, but by now they would have escaped and saved the day. But the Doctor haven't had the time to build and put forth a plan. Yes, he had a plan circling through his mind, but he hadn't started putting that plan into process yet. He always came back exhausted and ready to sleep, which was extremely rare for him considering he never really slept a full earth cycle. His sleep cycle always, at the most, been a couple hours, every couple of days. Maybe even a week. But since they've been here, all the Doctor had done was go to the labs, return back to his cell, and sleep. That alarmed Donna.

The door slammed open,once more that day, and the steady march of feet echoed through the silent white halls. Donna stood up from her bed, once again, checking to see if the Doctor had returned. To her relief the Doctor had. The Doctor marched between the two guards, a sorrowful look on his face. To Donna, he looked like a sad, lost puppy. His brown eyes were wide and he looked miserable. The Doctor was soaking wet. His brown hair plastered to his forehead, with drops of water flicking from the tips and trailing down his neck. He definitely had new clothes on. The shirt wasn't hanging off his shoulders quite as much and the pants fitted more snugly around his waist. He was still barefoot, except his feet were now wrapped in white gauze. He had a few dark bruises on his face and his hair was a bit singed on top, but other than that he looked put together, with no limbs missing. Donna breathed a sigh of relief, she was worried he would come back, completely mangled and unidentifiable.

The guards shoved him into his cell, before snapping the force-field up. They marched back down the hall and out the door. Donna turned towards her friend, who was kneeling on the floor, his head quirked down, and his back facing her. He looked absolutely miserable and that scared Donna that her Spaceman wasn't smiling or throwing jokes or reassuring her that everything was going to be ok.

"Hey Spaceman," she said calmly. She didn't want to upset him, but she knew he needed to talk about what happened. She was also curious, as well. The Doctor didn't acknowledge her greeting. Instead bowing his head lower and sniffed. Now Donna knew something had happened, possibly something embarrassing. The Doctor was never this quiet. She sighed, preparing herself for either a tragic story or a stubborn, heated argument about him being fine and her disagreement to that claim.

"How are you doing," she asked, she knew it was a stupid question, but she needed to start somewhere. He didn't answer. Donna brushed a hand through her red hair, her blue eyes still watching the Doctor intently. "Why are you wet?"

At that question, the Doctor turned around, his doe-like eyes staring at her. Donna could see all the anguish and sorrow flashing across his face. All the different emotions, the anger, humiliation,frustration,self-hate, and insecurities all playing at once. The Doctor parted his lips, to speak, and in the quietest whisper, she barely made out what he said, "I hate the showering room."

Donna quirked an eyebrow, her face softening, she wanted to comfort him but couldn't. So, the best thing she could offer him was a chance to tell his story. She leaned forward, showing him that she was there, to listen and help him through whatever had occurred.

"What happened," she asked in the most comforting tone of voice. The Doctor shook his head, biting his bottom lip. She could tell he was holding back tears, trying to be strong for her and not crumble. "Shhh," she soothed, "take your time. I'm always here to listen."

The Doctor buried his face into his hands. "I am so weak," he softly cried.

Donna shook her head in disagreement. Her heart broke, seeing her strong Spaceman, in such a depressed state. "No you're not," she replied softly, "You're the strongest man I've ever met."

"No I'm not. I am weak and pathetic and can't do anything right," he cried out in frustration. Donna for the first time saw all of his insecurities. The mask had slipped and what stood in front of her was a very broken man, with many regrets and horrors he had faced throughout his lifetime. "Even my own people didn't want me. I was shunned, exiled, a complete outcast all because I was different." Donna felt her heart shatter a bit more, this was the most he had ever revealed to her. She had only heard the good things about Gallifrey, but she never assumed that he was rejected by his own people.

"Oh, Spaceman," Donna whispered.

"I'm a monster," the Doctor said, wringing his fingers and chewing his bottom lip. Drops of water slid down his pale face.

"No you're not," Donna responded, " Why would you say that about yourself?"

The Doctor glanced over at Donna, tears brimming his eyes, but refusing to fall. He wiped them away, raising his head high. She knew, he was going to talk. Tell her, his true feelings. He needed to get this emotional weight off his chest and she encouraged it. He sighed, all the tension releasing.

"I had my first day of training," the Doctor begun, "Basically had to climb through a Jungle gym that wanted to kill me. There were these robots..." The Doctor paused for a second. "I killed every last one of them, I didn't give them a chance to make a choice."

Donna stared at the Doctor. Robots. He was upset about destroying a few robots. Donna shook her head and quirked her brow. "Robots, Doctor?" she asked, "This is 2015, I don't think robots have sentient intelligence, at this point in time. I don't think you should be upset about destroying a few robots, Spaceman?"

The Doctor shook his head, sniffing. "I know that. But what scared me was the way I felt about the whole situation."

"How did you feel?"Concern rose in Donna once more. She leaned forward. The Doctor gave a bitter laugh and leaned back against the wall.

"I enjoyed every minute of it," he replied, "I loved the chaos and explosions and watching the light flicker from their eyes. It was the same glimpse of power I felt when I destroyed the Racnoss, the cyberman, the family of blood, the daleks, and so on. That power hungry craze. The realization that I am the most powerful being in the universe and I can do whatever I like. That's what scared me."

Donna didn't know what to say. So, she stayed quiet and allowed the Doctor to finish.

"I felt the darkness, I knew I was capable of," he continued, "and I wanted to embrace it, but I held back. It was wrong. A single thought ran through my mind, what if it was people next. What if, I found so much satisfaction in destroying those robots, that next time I willingly killed a person without a single thought. I know I'm capable of it. Why do you think I received the name, the destroyer of worlds. That is why I'm a monster."

The Doctor sighed, rubbing at his eyes. He knew he probably scared Donna away and wouldn't be surprised if she wanted to leave after all of this. Who wanted to stay with an ego maniac, possibly insane, man. She had not answered yet and that concerned him. Maybe she was already scared and didn't want anything to do with him anymore. He risked a glance over at Donna, expecting fear and disgust, instead he was met with a compassionate smile that warmed his hearts.

"That doesn't make you a monster," she replied comfortingly. The Doctor quirked an eyebrow, a confused expression on his face. She smiled softly at him and continued, "You felt the darkness, but you refused to embrace it. That makes you stronger than most people,Doctor. To have this power, but use it for the benefit of others and not to satisfy your needs. You're the most selfless person I have ever met and I know you're afraid, but you don't have to be. I will always be here for you." Donna quirked her eyebrow playfully. "I promised you forever, didn't I?"

The Doctor laughed softly and nodded his head. He glanced up at Donna, a solemn look crossing his face. "But what if..."

Donna threw a hand up, pausing his question. "That is only a what if, I don't think you have anything to worry about, besides I'll slap you back into shape, if I even notice any of that nonsense, skinny boy," Donna exclaimed, wagging her finger playfully.

The Doctor nodded his head and grinned, laughing softly. The quiet laughter died down and they stared at each other thoughtfully. A frown formed on Donna's face and she quirked her head to the side. The Doctor immediately noticed the inquiring look she got, when she remembered a statement or a clue. She was so observant sometimes and the Doctor never could get anything past her. She always knew. The Doctor sighed, brushing a hand through his hair, and muttering silently to himself. Her eyebrow had quirked. Great.

"You want to know about the comment I made about the showering room, don't you," the Doctor asked, a lump forming in the back of his throat. He didn't want to talk about, but he had already revealed a lot about himself, one more humiliating story wouldn't hurt. He crossed his arms, bowing his head slightly. Donna noticed the position, she snapped out of her curiosity, and immediately went into comfort mode.

"Shhh, Spaceman," she soothed, "you don't have to tell me anything. I just wanted to know why you were wet and understand your dislike for the showering room. But I don't have to know if its humiliating for you to tell."

The Doctor shook his head, tears forming in his eyes again. Rassilon, he felt like an emotional teenage girl today. He wiped his eyes, cursing his weakness. His emotions felt like a wayward roller-coaster, but he needed to tell somebody and Donna was his best choice. He sighed again, trying to relax, but he felt horrible and sick.

"Rassilon, I hate the showering room," the Doctor muttered. Donna smiled encouragingly, but she was worried for his well-being. "It was my reward," he began, "I had beaten the course and Major Johnson said I was going to be rewarded for my success. He said I earned a stop at the showering room. I was excited. It was a chance for me to take a warm shower and wash the blood and sweat from my skin..." He gulped, his cheeks turning a light pink. Donna frowned, something was not right. "It wasn't anything like that. It was horrible and degrading..." he sniffed, choking on his emotions, and biting his bottom lip. He brushed a hand over his eyes, trying to clear the blurriness that was caused from unshed tears.

"They dragged me into this cold stone room. The ground, slippery and wet. The two men ordered me to strip. At first, I wasn't to keen on stripping in front of them, but after a while I really wanted that shower..." The Doctor's shoulders trembled. "I stood there in the middle of the room, naked and shivering. I was scared, I shouldn't of been, but I was. One of the guards left, leaving the other alone with me. He said nothing, just stared, jeering. It was humiliating..." The Doctor hiccuped a sob and Donna wanted to hug him. This was the type of stuff, she was afraid that would happen. Donna sighed deeply, readying herself for a tough question.

"Did he touch you,"she asked, a tremble in her voice. She didn't want to hear the answer. The Doctor shook his head.

"No, not in the way you're thinking. Besides, I would of fought back if that were the case," the Doctor replied. Donna let out a sigh of relief. If it turned out something like that did happen to her Spaceman, she wouldn't hold herself accountable, if she rung the necks of every lousy, sadistic bastard in this place. She was loosing her temper and she could feel the familiar heat rising to her cheeks. She needed to calm down, for the Doctor's sake. She wouldn't be much use to him, if she lost her cool. Donna closed her eyes counting to ten, before snapping them open. The Doctor watched her in concern. That was so him. He was the one having a horrible day and he was more concerned about her well being.

"I'm ok," Donna stated calmly, "go on. What happened?"

The Doctor nodded his head slowly. "The second guard came back with a hose. He stared at me with disgust. Like I was nothing better than the scum on his shoe. They hosed me down, like a dog. Spraying me with freezing, cold water. The water pressure was on high and I was thrown against a wall. They moved closer and switched off the hose. I was shivering cold and...and...and." He rubbed his eyes again, humiliated tears flowed down his cheeks. He wrapped his long arms around his stomach.

"They washed my hair with cheap soap. Rubbing it into my scalp. I fought back a little, but that only earned me a swift kick to the side. I felt like an animal and I'm sure that's how they wanted me to feel. Once they finished soaping up my hair, they blasted the water at me again. Washing the soap away. I was wet, cold, and embarrassed, curled up on the stone floor." The Doctor gulped again, his ears were bright red, and his eyes puffy. Donna gaped. She couldn't believe the cruelty she had just heard. No one deserved that. The Doctor coughed. He was absolutely miserable. "The two guards pulled me up, one running his hands through my hair, to make sure all the soap was gone. They dragged me away from the wet floor, dropping me down somewhere dry. They grabbed some clothes and tossed them at me. They watched the whole time, as I got dressed. Not making a peep, except for the occasional vulgar comment. I didn't care anymore. I just wanted to leave. They dragged me back to my cell and here we are now." The Doctor looked down at his hands in his laps, he didn't have the courage to look Donna in the eyes. What happened was horrible.

"Oh, Spaceman," Donna said with sympathy, "I'm so sorry." Tears formed in her eyes. She couldn't even imagine the humiliation. He didn't deserve this. She watched him cry, for the first time.

Each tear-jerking sob, breaking her heart a little more. How could somebody do this to him? He rocked back and forth, trying to comfort himself, but what he needed was her and Donna couldn't get over to him at the moment. She angrily banged on the wall, cursing the name of this whole organization. She wanted to hug him and kiss the humiliation and anguish away.

What type of friend was she? She couldn't even comfort him or tell him everything was going to be ok. All she did was stand there, like an idiot, watching him cry. She hated this, she hated these people, this cell, evil, she hated everything. But most of all she hated herself. She couldn't do anything, she was only a stupid human, who listened to her best friend's tragic story, and couldn't do anything about it. She glanced over at the Doctor, his body still shaking from all the suppressed emotions, his face was red from sobbing, and he was now doing the choking, hiccup sob, since there were no more tears to be shed. He got to his feet, stumbling over to his bunk, and curled up on the thin mattress. Donna wiped away a tear from her cheek.

"Just rest, Doctor,"she whispered, "Everything will get better soon. I promise we'll get out of here and shut this place down for good."

The Doctor nodded his head, tiredly. His eyes drifting closed. The sobbing had taken a lot out of him.

"I know," he whispered back.

Donna watched him fall asleep, she bit her bottom lip, and sat down on her own bunk. She laid her head on the pillow, closing her eyes, as well. She fell into a restless sleep, her thoughts continually waking her up.

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**I hope you enjoyed. I know the Doctor is a little ooc, but I thought it appropriate for a situation like this. Please review and I will hopefully update again tomorrow. Thank you again for all your wonderful reviews! :D**


	12. Chapter 11

**Please review! I love reviews!**

Chapter 11

**Six days later:**

"Now fold it like this," the Doctor explained, as he folded the blue paper creating a smaller box. The Doctor was propped up against the right wall of his cell. The last few days had been especially tough on the time lord. Training had been five hours a day and an extra five hours if he failed the course that he was told to do. Major Johnson had made each training course more difficult,to almost impossible,to get through since the Doctor had proven to be agile and resourceful. The Major had also begun training him in different hand to hand combat techniques, so spending long hours in the boxing ring wasn't unheard of. The Doctor always attacked lightly which caused the Major to believe the Doctor was weak and inexperienced. What the Major didn't realize was that the Doctor was already well versed in many of these fighting techniques, plus had a few other martial art styles, from different planets, to use. Overall, the Doctor could easily take down Johnson, but he was afraid to. He didn't want to hurt the human, no matter how greatly he disliked Johnson.

"Like this, Doctor," Bobby Mills, the janitor, asked. The Doctor glanced over at Bobby, surveying the janitor's tiny box. It was slightly wrinkled, but he had done an excellent job folding it. The Doctor smiled warmly. Him and Bobby had grown very close in the past week or so, since he and Donna had been here. Bobby had proven to be a true ally. He willingly helped the Doctor, with his escape plan and in return the Doctor taught Bobby how to create origami animals or played boardgames with the kind man. In was nice knowing that there was, at least, one decent human in this place.

"Yep, just like that Bobby," the Doctor responded. He folded his paper again and Bobby copied. "You're getting better. I think this is your best origami crane yet."

Bobby smiled widely, he puffed out his chest proudly, pushing up his glasses. "Maybe you can teach me other origami animals. Like a dragon or a crab or a butterfly."

"Of course. I'm not going anywhere anytime soon," the Doctor replied. The Doctor poked out his tongue slightly, as he folded another part of the paper. Bobby copied the Doctor's facial expression folding his paper as well. The Doctor glanced up at Bobby, noticing his expression. He grinned brightly.

Picking up the bowl next to him, the Doctor grimaced as he took a bite of the gray goop they called food. He squeezed his eyes tight as the goop slid down his throat. Bobby watched him curiously, pushing his glasses up his nose, and straitening his beanie.

"What does that stuff taste like," he asked curiously. Quirking an eyebrow. The Doctor shook his head, choking, and wagging his tongue in hopes of ridding the terrible taste.

"Terrible," he blurted out, "I don't even know what it is. But it taste terrible." He could really use a mint right about now. Bobby crinkled his nose in disgust.

"It looks terrible," he replied, covering his nose slightly, "Smells terrible too. Do they really feed you that stuff?"

The Doctor nodded his head, his face tinged a light green. He always felt sick after he swallowed a bite of the goop.

"Yep," the Doctor stated, popping the p, "Nothing like a bit of snot, mixed with toxic waste to make your toes curl."

Bobby's eyes widened in innocent horror. "They feed you snot and toxic waste. I am so sorry," he apologetically exclaimed, "How are you even alive?"

"Well...um," the Doctor stuttered. He leaned his head against the wall, "It's not exactly that." Bobby watched him curiously, as the Doctor tried to collect his thoughts.

"Oh for God's sake,"Donna exclaimed. She glanced over at Bobby who had turned around to face her. "Bobby it's not snot and toxic waste. Its a nutrient pack that they mix with water and heat up slightly to feed everyone. It's not going to kill him. He's just being dramatic."

The Doctor leaped up at the accusation. "Oi! I have a right to be dramatic," he exclaimed, a playful twinkle in his eyes. Donna noticed the spark and smiled. "You're not the one eating it everyday!"

Donna playfully rolled her eyes. "Oi! I do so have a right to complain. I've had badly cooked chicken and potatoes for a week or so straight. I go to bed sick each time I eat them! So, don't give me any of that nonsense, skinny boy!"

The Doctor did a comical gasp, throwing his arm across his forehead. "Oh, the horror," he exclaimed, "badly cooked chicken and potatoes, how will you ever survive."

Donna cracked up, at the dramatic flare, to the Doctor's tone. She clutched her stomach, as merry tears trailed down her cheeks. It was a different experience considering the ones they've been having lately. It was nice to see the Doctor laughing again. Donna snorted, before covering her mouth still giggling. She straitened her face, trying to look as serious and intimidating as possible, except the small smirk at the corner of her mouth gave her away.

"Oi, Sunshine," she shouted. The Doctor peeked an eye at her, a smile still on his face. They both needed this familiar banter it had been a while. A cheeky smile played at her lips. "This meat could of come from some parasite infested bird, that lived in some rural muddy area. The potatoes were probably rotten as well and came from the same filthy place the bird did!"

Donna cocked her eyebrow, she smiled cheekily in a silent expression of 'beat that, Spaceman'. The Doctor grinned competitively, excepting the challenge. He took a huge gulp of air, preparing for his long winded counter attack.

"Well," he dramatically enunciated, "the sludge that I'm eating comes from the mud that is stuck to the bottom of that parasite-infested bird's foot, which is actually toxic waste. Which caused those potatoes, you're eating to rot." He gave a smug grin, crossing his arms triumphantly, before adding, "Oh yeah, the toxic waste had, also, created giant, hairy, man eating worms that leave slime trails throughout the toxic mud creating the grayish appearance. The cook than scrapes the slime covered mud up, plopping it into a bucket, and cooking it steadily over an open fire. Plus, the sludge is alive! I swear, I've seen it squirm and burp! It's not pretty!"

Donna glared playfully. She crossed her arms over her chest, quirking her eyebrow. "Is that a fact."

That Doctor nodded his head, grinning triumphantly. "Yep," he stated,popping the p,"HA! I win!"

Donna shook her head, laughing. Bobby's eyes bounced back and forth between the Doctor and Donna. The argument was ridiculous and he didn't understand why they were arguing over who's meal was worst when they both sounded pretty disgusting. Who would want to eat sludge or parasite-infested birds anyway.

"Spaceman," Donna exclaimed, "You've won this argument long ago, nothing could compare to that stuff you're eating."

The Doctor laughed. "I know, I'm just very competitive and needed a good banter. Thanks."

"No problem," Donna stated, still giggling slightly, "I love a good banter, especially with someone who can stand their own grounds, in the debating area."

The Doctor nodded his head. He stared thoughtfully at Donna. Everything had gone quiet, except for the soft snickers of some of the other cell-block occupants. Donna grinned.

"I think we provided good entertainment this evening,"Donna stated theatrically.

"I believe we have Ms. Noble, excellent show," he responded just as dramatically.

"Why thank you Doctor," She said. She turned to the other prisoners and raised her hands, "We're here all week and possibly next week!"

"Literally," the Doctor added. Everyone stared at them blankly, before Amarzylda and a few others begun clapping their hands and laughing. The Doctor winked at Donna and gave a dramatic bow. Donna copied. Bobby looked at them blankly and shrugged. He didn't understand those two sometimes, they were strange. But, at least, they were his friends. So he never judged their ways. The Doctor sat back down, listening to the chatter, that had started, among the other prisoners. They, too, were now laughing and making jokes. The Doctor smiled. At least he and Donna broke the scared silence. The Doctor winked at Donna. She nodded her head, in understanding, giving a thumbs up. There was a slight cough and the Doctor turned to look at Bobby. He held out his origami paper.

"What next?" he asked. The Doctor grinned, picking up his own paper.

"Now you fold it like this." the Doctor folded the paper again. He slowly created a crane and Bobby copied each move, with intense concentration. The Doctor folded and formed the last bit.

"There," he exclaimed, holding out his crane. Bobby finished his own right after, holding it out as well. A gigantic grin brightened his features. Bobby stared proudly at his crane, before facing Donna.

"Hey Donna, look! I created a crane," he exclaimed,"I think its better than my first."

Donna clapped her hands and smiled. "Good job, Bobby. You're getting really good at that."

Bobby beamed with pride. The Doctor glanced over, with a mock hurt look. "Don't I get a congratulations, Donna?"

Donna rolled her eyes. "If you want," she stated exasperated, "Good job, Doctor. It's not like you knew how to make paper cranes to begin with."

The Doctor laughed, his brown eyes twinkling with amusement. "Oh,chucks, Donna, you're making me blush."

Donna chuckled, quirking an eyebrow. "Oh, Chucks, Doctor?" she asked teasingly, "You're making me blush?"

"Just go with it," the Doctor stated, "I don't plan on ever saying that again."

Donna shook her head, with a cheeky smile. "Adding it to the mental list of things the Doctor shouldn't say. You know Spaceman, this list is getting rather long."

"Oh, shut-up," the Doctor retorted back good naturedly. Bobby grinned at the two, before twirling his crane. He looked down at his watch, his eyes widening.

"Doctor," Bobby shouted, distracting the Doctor and Donna from their banter. They both turned to the janitor.

"Yes," the Doctor responded calmly.

"I've got to go. It was nice talking to you and Donna. I'll try to visit tomorrow," Bobby explained. He bopped his hand against his head. "Oh, right! Almost forgot." he looked stealthily around the room, making sure the surveillance cameras didn't catch him. He pulled out a screwdriver and a wrench, including a few broken cellphones and wires from within his janitor suit. He glanced around once more and pushed it underneath the small crack between the force-field and floor towards the Doctor. The Doctor quickly grabbed the tools and electronics, hiding them under his shirt. He mouthed 'thank you' to Bobby and Bobby nodded his head in understanding, before getting up and leaving.

The Doctor watched Bobby leave, a soft smile on his face. He moved over to his bunk. Underneath the bunk, the Doctor had found a crack in the tile. He had moved the tile away, discovering a small hole. Since he had arrived here and Bobby begun to help him, he had been storing away all the electronics he received in that hole. Slowly, he had begun building the tool he would use for the escape. It had been a slow process and probably would last a few more weeks before it was all set up . It angered him that he haven't had the time, to fully focus on the plan and tool. But this plan required time, if he was going to get everyone out. He had made a promise and he was going to keep it. Even if he had to suffer at the hands of these monsters a little bit longer. He leaned against his bunk frame, rubbing his eyes. He was exhausted, more exhausted than he had ever felt in his nine hundred odd years. He must be getting old. The Doctor bitterly laughed, plopping onto his bed, wincing. He was going to shut this place down, the Doctor promised himself. If only he had a clue how.

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**Hi, thanks for all your reviews! Glad your enjoying this story. So, yes, this chapter was definitely more relaxed. I felt like there needed to be a slight break from the whump. I also needed to develop Bobby's character. :) I hope you enjoyed the banter and I hope you also review! Thank you again!**


	13. Chapter 12

**Please review! I love reviews!**

Chapter 12

The Doctor was marched towards a room. He had been woken up, by the guards, by a brutal kick to his side. His side was still throbbing with pain. He was exhausted. His brown eyes drooped lazily from waking up early. Yawning widely, he scratched the back of his head, brown hair sticking up in every direction. He had grown used to the silent walks.

The guards didn't talk much to him, unless they were Norris and his gang of antagonizers. Those three enjoyed making him angry, which caused him to say something stupid, which lead to him being beaten for his retort. It was an awful cycle, but he had difficulties breaking it. Thanks to his big mouth.

The Doctor stared straight ahead, doors were on both sides of the plain hallway, and like the rest of the place the walls were white, with white tiled floors. Even the scientist were wearing white. These hallways always made him feel distorted and confused, which was probably what the people in charge wanted the alien prisoners to feel. This place had a smothering feeling of hopelessness and captivity and the Doctor slowly felt himself being engrained to these feelings.

But he refused to give up. He would fight, down to his very last breath, to get everyone of these aliens and Donna out. Even if he didn't make it in the end. The Doctor held his head up high, refusing to get suck into his dark thoughts. Those thoughts always ended bad. But he found himself regularly thinking about his captivity, slowly losing the optimism he normally had. He found himself doing exactly what these people asked him to do and it scared him. Would he soon willingly murder someone if they asked him too? He didn't know, but he could feel himself changing and the changes were dangerous. This place was bringing out a darker side of the Doctor. A side that he had locked away deep inside his unconscious. He was afraid to tell Donna about these changes, since she hadn't noticed or mentioned it. He was doing an excellent job hiding his fears from her and he didn't want her to be burden with the worries of possibly a more dangerous Doctor. She knew he was dangerous ever since their first adventure, with the Racnoss, but she knew he had the capability of controlling that rage. But if these people were able to rip away his control, of his anger, there would be nothing holding him back and he knew that. These were the worries that plagued his mind everyday. That one day he would lose control. Who would stop him? It was part of the reason why he had sped up building his tool. Even exhausted, he would throw in an hour of building. That's all he could afford.

He was kept pretty busy throughout the day with the testing and training, that he normally got back pretty late and had already missed his only supper for the day. It was infuriating. Though the food was nasty, he was still hungry. The cook only came once and never came back to feed the alien prisoners who missed the first round. The Doctor, thanks to the Major and scientists, found himself missing meals quite often. He didn't need to eat as much as a human did, but going a few days without food was still uncomfortable. The Doctor shook his head, he never liked having his mind wander anymore. His thoughts always become pessimistic. He knew this place was changing him and it wasn't for the better.

The guards pulled him roughly to a halt. The Doctor stumbled slightly from the sudden jerk, before steadying himself, and glaring irritably at the guards. He was tired of being lead and pushed around and the anger bubbled deep inside his chest. The guards threw open the doubled doors and pushed him inside. Again, the room was huge. It was like every room in the Underground was huge. The room was white, the regular color for the Underground. Except this room had multiple doors and rafters, for climbing, as well as boxes and cracks and other objects all over. He quirked his head curiously, wondering why they brought him to a room like this. In the middle, of the room, stood his two least favorite people in the universe. Major Johnson and Dr. Carter. Which meant today was going to be terrible, since they were working together. Scientists were scattered around the room, all with clipboards and speaking to each other quietly. Probably discussing the experiment he was about to be put through. Brilliant.

Major Johnson stood stiffly, as the trio entered the room. His light, brown eyes cold, as he looked down at the Doctor. His arms behind his back and his chest puffed out. His legs were spread apart slightly and his chin was held high, a scowl evident on his face. Dr. Carter stood next to him. His hands clasped in front of him and his black eyes scrutinizing the Doctor. A creepy smirk, played at the corner of his lips. The Doctor gulped, walking hesitantly forward towards the two men. Since when did he started gulping? This was more evidence that he was changing. The guards shoved him forward, marching him right up to the two men. The guards pushed him to the ground, at Johnson's and Carter's feet, forcing him to kneel, with his hands resting on the ground. The Doctor stared up at the two men, as the guards marched away. He plastered a large grin on his face, trying to show that he wasn't intimidated by these two men. His knees were already sore from kneeling on the hard ground.

"Johnny, Cart," he exclaimed flippantly, "How's it going? Long time no see. Well, at least since yesterday or if you want to be specific five hours, twenty minutes, and three seconds ago." His grin grew wider, as he glanced between Johnson and Carter. "What do you have planned for me today. It has to be something that involves both training and testing. So, my guess is something physical. Possibly running. Or you mentioned, Johnny, something about reflexes. Are we going to test my reflexes today. Because that could be interesting...unhhh!"

Major Johnson stomped down his steel-toed boot,crushing the Doctor's hand underneath it. The Doctor bit his lip and squeezed his eyes shut. The Major grinded his boot into the Doctor's hand, bending down low. _Crack._ The Doctor gasped as he felt one of the bones break in his hand. He panted slightly, his eyes wide with pain. The Major's teeth were gritted in irritation, but his eyes were frigid. The Doctor's eyes shifted down to the floor. He tried to pull his hand away, but it only shot a wave of pain through his nerves.

"My name is not Johnny," the Major stated coolly, "It's Major Johnson to you. Is that understood."

The Doctor nodded his head quickly, his teeth gritted in pain. He glanced up at the Major and Dr. Carter both pairs of eyes coldly watched him. The Major pressed his boot down a little harder on the Doctor's hand. The Doctor whimpered from the pain, his eyes glazed over.

"You broke a couple of rules, subject 13," Major Johnson said calmly, his eyes burrowing into the Doctor's head. "What were they?"

Dr. Carter grinned maliciously, enjoying watching the Doctor's pain. He crossed his arms, his tongue glazing his teeth with saliva. His black eyes squinting dangerously, at the scene before him. The Doctor took a deep breath, trying to fight back the pain that he felt. He glanced up at Major Johnson, panting slightly.

"I was disrespectful," he responded back, "And spoke when I was not spoken too."

Major Johnson lifted his foot slightly from the Doctor's hand. The Doctor brought his injured hand towards his chest, cradling it with his other hand. He stared down at the ground. He felt weak and that caused him to flush with anger. His brown eyes darted up to Major Johnson. He glared angrily.

"Good," the Major replied condescendingly, "You do learn." The Doctor gritted his teeth in fury. He was so sick of being treated, like crap on the bottom of someone's shoe. He turned his head away, his face flushing even more with frustration. He closed his eyes remembering what Donna told him about how she controlled her temper. He closed his eyes and counted to ten. He could already feel all the tension leaving his body. He snapped open his eyes and glanced back at the Major. He felt a lot calmer. The Major and Dr. Carter watched him curiously, as he regained self control. Carter turned to Johnson, his eyebrow raised.

"I think it would be interesting to study Subject 13's emotions," Dr. Carter stated, "See what sets it off and how it manages to control its temper. Many of these alien's are incapable of controlling their anger, like a human can. I want to know how subject 13 manages it."

The Doctor glared. Of course, everyone here could control their tempers, they're just exhausted and angry. Thanks to all the test these scientists inflicted on them. The Doctor felt him slowly losing his temper again. He counted to ten once more. The Door slammed open and the clips of high-heels echoed off the plain walls. A woman the Doctor recognized, from the suffocation experiment, walked in. she had short brown hair and blue eyes. She walked stiffly over to the Major and Dr. Carter. Carter's grin widened.

"Ahhh, Dr. Black," he greeted, "So nice of you to join us today, in this little experiment."

Dr. Black glared coldly at Carter. She glanced over at the Major giving him the same look.

"I told you Dr. Carter," she replied, "I only came to take notes on subject 13. It was quite fascinating watching the last experiment."

"Not for me," the Doctor grumbled, earning him a swift kick from the Major.

"Well, you came on the right day," Carter stated, a sinister grin stretching across his face. "We're combining this experiment with subject 13's training. Hence why Major Johnson is present."

Dr. Black nodded her head, she pursed her lips and glanced down at the Doctor. Her cold blue eyes stared at him, like he was nothing more than a petri dish under a telescope. Something to study and learn more about. The Doctor watched curiously as his trainer and the scientists discussed the upcoming experiment. He didn't like where the conversation was heading. Major Johnson glanced down at him. The Doctor rubbed his injured hand nervously. He never liked that look.

"Subject 13, the test you will be doing today will involve testing your senses and reflexes," Major Johnson announced, "We are going to put you through several different scenarios. The first will be your sense of smell. I am going to give you a scent and you have to locate where it is in this building, while at the same time dodging rubber bullets. If you get hit by the rubber bullets more than six times you have training with me, and your privilege to food and water will be restricted for the day. Have I made myself clear."

The Doctor nodded his head, mumbling a quick, "yes, sir." He cringed slightly, not enjoying those words leaving his mouth.

"The second test will be testing your hearing. You will be blindfolded and your nose clamped shut. You have to stretch your hearing and navigate yourself around the building. I will give you a noise and you must follow that noise. As well as using your hearing to listen for other things. Again there will be rubber bullets and possible ambushes. Do you understand."

The Doctor nodded his head in understanding once more. The two scientists were analyzing his reactions and body posture, causing him to squirm under their scrutiny.

"The third test will be testing your eyesight. You will be in a dark room. Your ears will be plugged and your nose clamped shut, to avoid any cheating. I have read you can see quite clearly in the dark, we will be testing your night vision. Again there will be rubber bullets and ambushes. Afterwords, we will be testing your eyesight in a lighted area. We will calculating how far you can spot something, depending on the size. And you will describe the object to us. Do you understand?"

The Doctor nodded his head, rubbing at his eyes. He could just tell today was going to be a long day.

"The fourth test will be a lot simpler and not much physical work. We will be testing your tasting abilities. You will be blind, deaf, and unable to smell. We will give you several different substances to taste. You will tell us exactly what you tasted, listing the ingredient or type of taste it is. We will tell you how accurate you are. Have I made myself clear?"

The Doctor nodded his head, mumbling a quiet, "Yes,sir." before raising his hand slightly. The Major scowled at the Doctor and crossed his arms.

"What," Major Johnson growled, his lips curling up in a sneer. He slowly reached for the baton at his side. The Doctor lowered his hand.

"I have a question about the smelling test," he responded, rubbing at his swollen hand. His eyes drooped with exhaustion. The Major nodded his head, allowing the Doctor to ask the question.

"Why am I not blindfolded and deaf for the smelling test, while all the other test you have prepared cancel out my other senses?"

The Major glared. He lifted his chin up, expressing his superiority. "Because I don't expect you to smell bullets and I want you to be able to focus on the main smell I provided you."

The Doctor nodded his head, his brown hair flopping all over. The Major pulled out a baggy with a white, dirty cloth inside from his pocket. He pulled out the cloth shoving it in the Doctor's face. The Doctor's nose crinkled with disgust as the smell wafted his nostrils. He pushed the cloth away, but the major stuck it back, into his face, forcing him to smell the putrid scent. After a few minutes of only smelling the disgusting smell, the major put the cloth away. The Doctor heaved heavily trying to gulp in as much fresh air as he could manage. Tears prickled at his eyes, caused by the terrible smell.

"Another cloth with the same smell is hidden in this building, you must locate it, as well as dodging rubber bullets and ambushes. We will time you and see how long it takes you to find this scent. If I am not pleased with the time, you will not be going back to your cell afterwords, instead spending another couple hours with me and losing your food and water privileges for the day. Same rules imply with the bullets, as I have mentioned before. Have I made my self clear."

The Doctor nodded. His nose was already in the air, sniffing. He could smell the putrid scent slightly.

"Than go," Major Johnson ordered.

The Doctor complied, already walking out into the large room, with the many doors and rafters.

* * *

**Hope you enjoyed this chapter and thanks for all your review! :D The next chapter will be very action pact and a lot longer. So, hopefully I can get it out by tomorrow. Thanks again for all your reviews and I hope you keep reviewing! :D**


	14. Chapter 13

**Hi, so what I have decided to do with this chapter's test is to split into four short chapters, testing each sense individually. It made more sense and it would make it easier to describe whats happening. :D Please review! I love reviews!**

Chapter 13

_The Doctor nodded. His nose was already in the air, sniffing. He could smell the putrid scent slightly._

"_Than go," Major Johnson ordered._

_The Doctor complied, already walking out into the large room, with the many doors and rafters. _

The Doctor took a long sniff, his nose twitching with the familiar scent as well as several other different scents assaulting his nose. His eyes searched the room, looking for any possible attacks. There were none at the moment, but he stayed on alert anyway. He circled a box, sniffing it, before shaking his head.

"Nope, he stated to himself, "Too sweet. A pastry smell. Smells like..." he took another long sniff. "A cake? Chocolate cake. Why would they have chocolate cake?" the Doctor quirked his eyebrow, before shaking his head. "Nevermind that. They want me to find a cloth with a putrid scent. These are probably scents that are here to throw me off or distract me." he turned away, walking further into the large room, his nose twitching the whole time, distinguishing the different smells. Some were sweet, others sour, some smelled fishy, and other smells were putrid, but none were the correct putrid smell he was looking for.

_WHIIZZZ._ The Doctor leaped out of the way of a speeding bullet. It hit the metal wall, bouncing off. The Doctor glanced around, noticing he was in some type of corridor, he was so focus on finding the smell, he wasn't paying attention to where he was going. _Whiizzz, whiizzzz, whizzz. _Several bullets shot off, flying quickly at him. The Doctor dodged each one. He twisted his body, the first bullet skimming right past him. He leaped over the second, before quickly rolling into a ball, and somersaulting down to the ground, landing on his feet and bending backwards for the third. The third bullet flew over the Doctor's chest, before bouncing off the wall behind him.

The Doctor straightened up, flattening out his somewhat dirty shirt. A cocky grin on his face.

"Well, that was easy," he exclaimed. Sadly, that was the wrong thing to say. A whole raid of rubber bullets, flew towards him. The Doctor frowned. "Great," he muttered, "I need to stop jinxing myself."

He took a long sniff, making sure the putrid smell was somewhat close by, before flipping over the first bullet. Landing gracefully on the ground, the Doctor begin to run as fast as he could down the corridor. He planted a foot on the wall, pushing off and spinning over a third. He landed on his feet, before bending, missing a forth and twirling out of the way of a fifth. He quickly bounded out of the corridor.

He was ambushed. He gritted his teeth, staring at all the guns and lasers pointed at him when he had left the long white corridor. They were attached to the wall. He was getting close. It had already been ten minutes since he started this test and he didn't know the time limit. _Smack. _"Oof." the Wind left the Doctor's lungs, as a bullet hit him in the solar plexus, he tumbled to the ground, as more bullets begun flying his way.

The Doctor breathed deeply, gritting his teeth. Sweat trailed down his face and he rolled out of the way as more bullets came flying at him. Five more hits and he would be forced to train with Major Johnson for two more hours. Better not get hit again.

He jumped back up and stared at the bullets, a slight smirk on his face. He forced time to slow down. He heard the slow bang from the automatic gun. A low rumble that shook the ground. He watched as the bullets, slowly were released from the muzzle, exiting the black abyss of the barrel. He heard the quiet bounces of bullets hitting the wall and falling to the ground. The bullets whizzed past him as he sidestepped each one. He could see the movement in slow motion, the timing. The small gray, swirly trails the bullets left behind. He jumped slightly up and quickly twirled out of the way of each bullet. Bending and twisting, jumping and flipping. He dodged each bullet, quicker than the eye could blink. He felt his hearts pumping, as adrenaline raced through his veins.

Two advanced on him at once. One from the bottom and one at top. The Doctor jumped, twisting his body to the side, which made him look like he was laying down. He forced his body to twirl a bit and both bullets passed him. One flying over his chest. The other under his back. He curled up and fell to the ground in a somersault. Jumping to his feet.

He lifted his nose and took a sniff, the putrid scent was closer. Twenty minutes had passed. He flipped over a laser that buzzed right at him, standing on his hand, he gracefully fell back to his feet, placing a hand on the ground.

He brought time back to normal speed. The quick patters of bullets hitting the metal wall, echoed throughout the large building. A grin lit his face. He stuck his nose in the air again, nostrils flaring as each new scent entered, his brain quickly categorizing the different smells, trying to locate the right one. The room was filled with different scents and it was slightly overwhelming, but he had to find this putrid smell. He pushed all the other scents away and quickly locked onto the requested scent. His brain had found the scent that matched the cloth he smelled.

He stood to his feet, his eyes quickly scanning the surroundings for more possible ambushes. A determined smile lit his face. The Doctor sprinted towards the scent, the smell growing stronger the closer he got. He stood in the middle of a room, spinning around. The scent was close, but he didn't know where. He pause for a second. Twenty seven minutes had passed. He probably would have already found the cloth, if he wasn't dodging bullets. He closed his eyes and breathed in deeply. He could feel the smell particles entering his nose. He twitched slightly trying to pinpoint the exact direction. His nose crinkled from the unsatisfying smell. His eyes snapped open. A smirk ticked at the corner of his lips. His eyes shot up to the rafters above.

He didn't know how far he was from the room he began in. He wasn't paying attention to the corners he turned or the doors he opened. He was too focused on the smell. The Doctor glanced around quickly making sure nothing would randomly pop out and shoot him. He turned his gaze back up to the rafter which possibly held the cloth. Thirty-two minutes and fifteen seconds had passed. This was getting to long for his liking. He bounded over to some wooden crates that were in the room. Climbing to the top of of the crates, he glanced around once more making sure nothing was going to attack him. He bent his legs and leaped off the boxes. He grabbed onto the pole and quickly pulled himself up, flipping onto the rafters.

The rafters were white, with tons of metal boxes and benches crowding around. The Doctor crouched, placing his left hand on the ground to keep him steady, he scanned the rafter, taking a long sniff. The putrid smell was definitely up here. The smell had grown a lot stronger. He glanced around looking for any signs of the automatic guns. He didn't hear the clicks, so he assumed it was safe to step out into the opening. stepping out silently, his feet barely touching the ground, as he gracefully bounced along the hard metal floor. His nose in the air. The smell blasted his senses, causing him to stumble back, and clutch his nose. Tears prickled in the corner of his eyes. He coughed.

"Yep," he wheezed, "Definitely up here. Better find it." he slowly let go of his nose, sniffing the air once more. He coughed more violently as the smell viciously attacked his senses. He twitched his nose slightly, following the scent, he got on his hands and knees. Taking a large whiff, like a bloodhound would when looking for its prey. There was a cracked section inside the metal floor. He crawled over, the smell growing stronger with each approach he made. He halted at the crack and reached his hand inside. Pulling out the white cloth saturated in the disgustingly vulgar scent. A grin split his face, as his hand came up and covered his nose. The smell was absolutely nauseating. It reminded him of death and decomposing bodies and it powerfully hit his smell receptors. He had found the cloth in thirty-four minutes and fifteen seconds. He took a big gulp of air, inhaling through his mouth.

"I FOUND IT!" he shouted to the scientists and Major Johnson, wherever they were. Hopefully they could hear him. He didn't want to lose his supper privileges today. He frowned as the thought crossed his mind. He really was changing. "IT TOOK ME THIRTY-FOUR MINUTES AND FIFTEEN SECONDS!" He waited for an answer but none came. The Doctor stood up and walked to the edge of the rafter. He glanced down, before jumping to the bottom and landing softly on his feet. The rag was still grasped tightly in his hand. He looked around, waiting for Johnson to answer. "DID YOU HEAR ME! I SAID I FOUND IT!" He twirled around, before shrugging his shoulders, deciding he should head back the way he came anyways. He heard a low buzzing noise and a voice switched on.

"Subject 13 return back to where you have started," the voice, on the other end, ordered. The intercom switched off and the Doctor shrugged his shoulders, heading back through the maze of doors and corridors towards the room he had started in.

* * *

Major Johnson and Dr. Carter were impressed with what they had witnessed from the surveillance cameras that followed subject 13's every move. The creature was extremely quick and they found themselves replaying the ambush scene over and over again. Dr. Carter grinned with fascination, his beady black eyes wide with awe. He had never seen a creature move so quickly. It was like it slowed down time. The only time it was hit by a rubber bullet was when it wasn't paying close attention.

"It moves like a feline," Dr. Carter exclaimed, his grin widening, "The way its body twisted, no human alive could ever do that. And the quickness of its motions! It was like subject 13 could sense every bullet that flew towards it, before the bullet even left the gun!"

Major Johnson grunted an affirmative. "I need to create a harder courses for it. Put those quick reflexes into its fighting skills. I believe its been holding back on me."

Dr. Black stood far off from the two men. She had watched the video several times and knew subject 13 would be an interesting specimen to study in her upcoming drug test. She needed to schedule a time to bring it in. She had so many plans for it. She glanced over at Major Johnson, with a cold glare. "Major, are you suggesting making his training hours longer. That might eat into the scientists time with it."

The Major glanced over at the stone faced woman, before turning back to watch the monitors. "Yes, it might. But we can also cut back its sleeping and relaxation hours. it doesn't need that much time in its cell. Besides, It needs to work harder and I haven't even started training it with weapons yet. The Colonel wants subject 13 obedient and a trained killer soon." Major Johnson leaned against the monitor, coldly watching subject 13 approach. The creature held the rag in its hand. The technician who was watching its every step, had handed the Major a piece of paper with information on how long it took subject 13 to find the rag. He glanced back over at Dr. Black."But I am willing to find a solution. What you and all the other scientists do here is extremely important to Earth's technological development. We don't want to be stuck behind in our advancements if aliens, at some point, decided to invade."

Dr. Black nodded her head stiffly, excepting the Major's solution. As long as it didn't cut into her testing time, with subject 13, she was fine.

The Major stiffly marched over to subject 13 who had just arrived. A bright grin was on its face. Disgusting.

* * *

The Doctor was pleased with his accomplishment, he had found the cloth, while also being forced to dodge bullets. A very difficult feat. He couldn't help the grin that stretched across his face, as he rocked back and forth on his heals. Major Johnson approached him, with a scowl. The Doctor didn't let the Major's bad mood spoil his good mood. He held out the cloth and waved it around, showing the Major he had indeed found it. The Major stood in front of him, staring intimidatingly into the Doctor's brown orbs. He snatched the rag away, tossing it to the ground. _Slap. _The Doctor stumbled back as the Major powerfully backhanded him across the face. The Doctor clutched his cheek in shock. Had he done something wrong? The Major snarled, grabbing the collar of the Doctor's shirt and pulling him close.

"Wipe that smile off your face, alien," the Major growled, "Does this look like an amusement park to you!"

The Doctor quickly shook his head. Surprised from the violent reaction he had received, from the Major, when he had done nothing wrong. Johnson glared coldly, before releasing the Doctor's shirt.

"Thirty-four minutes and fifteen seconds," he stated icily. Glaring at the Doctor. The Doctor raised his chin defiantly. "I think you could of done better."

The Doctor gaped. Anger bubbled inside of him. He gritted his teeth. "I did the best I could," he growled back, anger blazing in his eyes. "Considering bullets were being shot at me and...Oof!"

The Doctor collapsed to his knees, as a baton was slammed into his guts. He gasped, clutching his slightly swollen abdomen.

"Don't talk back," the Major stated. Slamming the baton in the palm oh his hand. The Doctor gritted his teeth and stared daggers at the Major. The Major bent down slightly. "You've been holding out on me," he growled angrily, "Starting today after this little experiment. You'll be training with me for a couple hours. You won't be loosing your food and water privileges though, since you only got hit once by a bullet. But than again we'll see what happens in the next three experiments, now won't we."

The Doctor glared and slowly nodded his head. The Major grabbed the Doctor's shirt collar and hoisted him to his feet. He pulled out a blindfold and a nose clamp. "Next test. Testing your hearing. It will be similar to smelling test. You will be locating this sound..." the Major pulled out a recorder and switched it on. A low pitch, buzzing noise was heard. Its pacing was separated by at least a second. The Doctor listened to the noise, his brain filing it away to use later. He glanced up at the Major and nodded his head in understanding. The Major stared coldly, before switching it off. "Good," the Major stated. He walked over to the Doctor, tying the black blindfold around his eyes and placing the clamp on his nose, forcing the Doctor to breath through his mouth. The Major stepped back, his hands behind his back and chin held high.

"Your test begins now," he ordered, before swiftly turning on his booted heel and marching back over to the scientists.

The Doctor waved his hands in front of him, feeling around the blackened room. He Stretched his hearing out, trying to locate the buzzing noise. Like before the buzzing was farther away. He sighed, stumbling off to listen for the noise.


	15. Chapter 14

**Hi, I wanted to thank everyone for the wonderful reviews! It really made my day. :D I'm glad you all enjoyed the bullet scene it was one of my favorite chapters to write! Thank you again! Please review! I love review! :D**

Chapter 14

_The Doctor waved his hands in front of him, feeling around the blackened room. He Stretched his hearing out, trying to locate the buzzing noise. Like before the buzzing was farther away. He sighed, stumbling off to listen for the noise. _

The Doctor walked through the building once more, his arms out in front of him. He listened to the quiet buzz he had to find. He stretched his hearing, listening for any other sound in the silent darkness. He had not used his hearing as his primary sense for a long time, relying more on his eyesight and nose in the past. But now those two senses were out of the question and he had to search in the dark. The Doctor paused cocking his head to the side, his ears catching the sound waves of the buzz to his left. He could feel the small vibration along the floor, but because the vibration was feeble he knew it was a good distance away. His hands slid across a metal box, directing him in a different direction.

He paused, quirking his ear slightly to a new sound. He fell to his knees, placing his hands on the floor. He felt vibrations.

"Four marching," he muttered to himself, he laid down on the ground. His ears perked. He felt the the stomps of four pairs of boots approaching him. He listened. "Four men. Four heartbeats." He heard them pause. He expanded his hearing boundaries. Listening to the rustle of clothes, the helmets moving back and forth as the men turned their heads. He heard the metal boots, scraping across the metal floor. The silent click of gun, as the safety was turned off. The vibration tingled his skin and ears as the men began to search for him. Three new pairs of stomping metal boots approached the room, their steady heartbeats pounding in his ear. "And now there are seven," he whispered.

The vibration and noise outlined each man, as if the Doctor could see them. The sound waves connected with the Doctor's brain and drew a picture of what the room looked like and where each man stood. Each movement the men made, helped the Doctor picture the situation a little better.

_Ba-boom, ba-boom, ba-boom._ Was the steady rhythmic beats of the hearts. The soft steps vibrated across the floor, as the men searched for his whereabouts. He reached a hand out, softly patting the floor. He grabbed hold of something thin and metal, pulling it close to him. He focused his hearing for a second on the soft buzz he was looking for, before expanding his hearing radar once more, for the whole buiding.

He tapped the floor with the metal stick he grabbed. He heard the slow vibration across the floor, his brain lighting up the sound waves, the vibration hit the seven men, lighting them up as well, giving the Doctor a full sense of their postures and where their hearts were. He heard another click of the gun and he slowly got to his feet.

Turning his head, he listened to the silent beep of a machine. He banged on the walls and his whole blindness alighted with sound, he could here the silent chatter of the scientists in the room a few doorways down, the sound bouncing back to him. He listened to his two steady hearts beats, thumping like powerful drum. He banged on the wall again, sound waves creating a picture of the room once more. He heard the men turn their heads in his direction, and the scratching noise of fabric brushing against each other. All the noises were acute to his sensitive ears.

"There it is!" a man shouted. The Doctor clutched his ears, from the sudden shout. Normally, the shouting would not have effected him. But because he had his hearing on high, every sound was loud. Normally, he would keep his hearing on a normal 'human' basis or keep it lower when sounds got too loud.

He heard the guns clicking and the men approaching. He held on to his metal stick, dragging it along the wall. The sound vibrations shot off down the metal wall, lighting a way for the Doctor by using noise. He heard the grinding of teeth, as one of the men raised his gun. The three clicks of the trigger as it was pulled back and the loud bang that rumbled the room. The air brushed past the rubber bullet, as it sped towards the Doctor.

The Doctor's ears twitched as he heard the bullet fly towards him. He quickly twirled out the way, the vibrations softly brushing past the Doctor's chest and the gentle _clink _as the bullet smacked the wall. The Doctor turned sightless eyes towards the men. He listened to the heavy breathing and the pounding of the soldiers hearts. He didn't want to fight them. He grinned, trying not to look intimidating.

"I don't want to fight you," he said in a nasally voice, thanks to his nose being plugged. "How about you drop your weapons and leave."

The Doctor heard the guns click, as the triggers were pulled. The bangs echoed throughout the room, the sound waves brightening the room, in silver outlines, as the waves knocked against the walls. The Doctor could hear the bullets flying towards him, the sound bouncing back to his ears.

Like a graceful dance, he dodged each bullet. Twirling, twisting, bending, and flipping, similar to what he did in the last test. The Soldiers kept shooting, the Doctor using his ears, knowing where each bullet was directed. He clicked his fingers slightly, having dropped his pole when weaving through bullets. The clicking sound hit one of the soldiers, before bouncing back to the Doctor. He could feel the movements of the soldiers. He weaved around the bullets and towards the men with the guns.

The soft clicking of guns out of ammo bounced off the walls. The Doctor heard men shaking their guns and fiddling in their ammo pouches, looking for more bullets. The Doctor grinned, approached the men. Wind swept the Doctor's face as one of the men used their gun as a bat. The Doctor bent backwards, the gun swung over his chest. He reached out, yanking the gun from the man's hand and slightly twisting the soldier's arm. The others surrounded him. He heard a metal chain slide across the floor.

He pushed the soldier, who tried to hit him with the gun, out of the way. He jumped over the chain that snapped out at him. The chain hit the floor, with a loud _ching, _and the loud sound waves exploded into silver light. He quickly spun around, catching the metal chain in his hand and quickly yanking it out of the seventh soldier's hand. He could here the soldier fly forward from the strength of the yank, tumbling to the ground and quickly jumping back to his feet.

He twisted out of the reach of the men, sliding between the gaps he found using echolocation. He heard the first and second soldier smack heads together as he disappeared from their reach. Their bodies thumping to the floor unconscious. He twirled and twisted around the men, none were able to grab him. The Third kicked out his booted foot, trying to kick the Doctor in the head and knock him unconscious. The Doctor grabbed his foot and by using the man's weight, flipped the soldier onto his back.

The Doctor flipped out of the way of a fifth man. The fourth soldier grabbed his arm, attempting to hold the Doctor still. As the fifth soldier ran forward. Ready to drive his fist multiple time into the Doctor's chest. The Doctor jumped up, kicking the fifth man with both his feet. He fell backwards on the fourth, who was still trying to hold him still. He crushed the fourth beneath his weight. The Doctor did a backwards somersault off the soldier, landing on his feet. Stretching his hearing, he listened to the heartbeats once more and the blood pulsing through the veins of each soldier. All the men were still alive, except five had the steady heartbeats of men unconscious.

The Doctor turned his head to the sound of two men, trying to attack. The hairs on his arms prickled as they moved closer. He heard the cracking of knuckles and felt one of the men step behind him. They jumped at the Doctor, crashing to the ground. The Doctor was no longer there. Instead he was a few feet in front of the soldiers. Taunting.

* * *

The other two (the sixth and seventh) were still alert and throwing attacks at the alien, but continually missed. Subject 13 swerved quickly around the ambush. They couldn't keep track of its movements. The two men still held their guns and were shaking them menacingly, trying to scare the creature off. But, subject 13 had disappeared from the fight, when it lept behind a couple of boxes.

They couldn't find it. Why Major Johnson insisted they fight in the dark, they didn't know? The creature was already blindfolded and couldn't see a thing. At least they thought it couldn't. Their hands shook with fear. They had never fought something that moved this quickly. The soldiers eyes scanned the blackened area. How could they fight something when they couldn't even keep track of it? Sweat prickled at their brows and their heartbeats sped up with panic. They heard light footsteps and a slight bang from the right. They held their guns close. Their eyes searching for the blinded alien. It had already taken down the other five soldiers in less than four minutes. Without even being hit once. Were the others even still alive? They didn't know. The attack was so quick that they quite possibly could all be dead.

"And then there were two," it whispered menacingly in their ears. The soldiers gasped and turned their heads slowly around. Nothing was behind them. They felt the blood rush from their face, turning a ghostly white. How could something move this quickly? It was impossible. It was like a phantom. Untouchable. It struck like a serpent and moved with the grace of a feline. It was terrifying and supernatural. The soldiers glanced forward, their eyes widened in horror. The creature stood right in front of them, still completely blind. The Soldiers jumped, dropping their guns. They stiffened, gulping slightly. What was this thing? The Creature sightlessly stared at them, a grim look on its face. Even sightless it felt like the creature was picking thoughts from their heads. The creature quirked its head to the side, gracefully stepping towards them. It was like watching a predator about to finish off its prey. The men felt a new type of fear.

"I'm a Time-Lord," the creature stated, picking the question from their heads."And I am so sorry for what I'm about to do. I just don't want you attacking me again while I'm searching."

* * *

The Doctor lept forward at the two men. He sprinted towards them, hitting one in the temple and the other behind the neck. The two men collapsed simultaneously, knocking their heads against the ground. Unconscious. The Doctor fell to his feet, poising. his head bowed slightly and his arms spread out. He lowered his arms and raised his head. His ears catching the slow drumming of seven heartbeats. The soldiers were all unconscious.

"I am so sorry," the Doctor repeated. He stood tall, listening for the slow buzzing from the recorder. The noise came from the left. Twenty minutes had passed since the beginning of this test. He gracefully lept over the fallen men, wary of the weapons and bullets littering the ground. He followed the buzzing noise, trailing a lazy hand along the metal wall. He came to an opening between the wall, slowly stepping inside. The buzzing noise was growing stronger the closer he got. He was on the right track.

_Pit pit pit pit pit..._Was the sound of dozens of bullets being shot at him. The Doctor danced out of the way of each bullet. Swinging from side to side, flipping and twirling away from the bullets. He gritted his teeth as one sliced into his arm. He felt blood streaming from the wound. He ignored the sting, unwilling to be distracted. This was his second hit today. Four more and any privileges he may have had would be removed. He bent and twisted, as he danced among the bullets.

He heard the click of the automatic gun as a new round went off. Lights flashing behind his blindfold as his brain showed him where each bullet was. The gun's power caused the ground to vibrate with sudden blast of bullets. _Pit pit pit pit..._More bullets shot at him and the Doctor sprinted down the long hallway, avoiding bullet after bullet. He slid on his knees as one shot over his head. _BOOM..._a sonic blast shot over his head and he grabbed his ears as they begun to ring.

The Doctor lept up and continued his sprint, turning a corner rapidly. He had escaped the ambush zone. Breathing heavily, he wiped at his face. His hearts were racing. He stretched his hearing once more listening for the slow buzzing noise that he had_. Buzzz_. The sound was closer. The Doctor stood to his feet, his ears perked in curiosity. He bounded over to the sound. A smile gracing his face. He was so close. Twenty-eight minutes had passed. He was determined to find the sound faster than he found the smell.

He cautiously walked closer, his hands out in front of him_. Buzzz. _He took a quick right, the sound growing stronger. He patted down some metal crates. His hands wandering up and down. The noise grew louder. He leaned his head against one of the crates. His tongue poked out slightly with anticipation. It was in there. He moved his hand up to the crate and found it was shut closed. Frowning, his hands wandered along the crate, searching for a button to press. Instead, he found a hole. He reached in and grabbed the object with the buzzing sound. It was the correct object. The sound was a continuous buzz with a one second pause between each buzz.

The Doctor grinned widely. He had found the object in twenty-nine minutes and thirty seconds. A lot faster than the smell test. He held up the object for the scientists to see, panting loudly from the exertion his body put forth in this little test. He heard the familiar beep of the intercom switching on.

"Subject 13, you have completed the test," the voice stated, "You may take off the blindfold and nose clamp and return back to your trainer and the scientists." The intercom switched off and a loud beep sounded, telling everyone the test had ended. The Doctor sighed in relief, pulling off the blindfold and nose clamps. It was dark in the room and he blinked in surprise expecting the room to be lit.

"Probably didn't trust me not to peek," the Doctor murmured to himself. A huge smile split his face. "Easy peasy," he exclaimed.

The lights flashed on and the Doctor covered his eyes from the sudden brightness, as his eyes adjusted. He glanced around his surroundings before looking down at the object in his hand. It looked like a mix between a phone and an alarm clock. He switched it off. The noise was obnoxious to listen too. He glanced back down the tunnel he came from. He bounded forward, heading back to the scientists and Major. He whistled a merry tune as he retraced his steps.

* * *

The Doctor approached Major Johnson. Major Johnson stood with his legs spread out slightly and his hands behind his back. His chin was stuck up in the air and his light brown eyes glared down at the Doctor. The Doctor held out the clock/phone hybrid. The Major snatched it from his hand. He turned the object between his fingers, before tossing it away. His eyes coldly watched the Doctor. The Doctor evenly stared back, waiting for the Major to talk. He didn't feel like spitting out some witty comment, he was exhausted from the last two courses and needed to conserve energy.

"Twenty-nine minutes and thirty seconds," the Major stated indifferent, "A lot better than your first run."

The Doctor nodded his head. Adrenaline still raced through his veins, he was ready for the next exercise.

"And you got hit once," the Major continued, "Four more times and your losing privileges."

The Doctor rolled his eyes. Like he didn't already know that. It seemed like the Major enjoyed rubbing the fact, that he was property and had no rights, in his face. It was really obnoxious. _Smack. _The Doctor's head flew to the side, as a fist was driven into his bruised face. The Doctor turned his head back to the Major, glaring defiantly. This time he didn't groan from the pain. Johnson snarled.

"Don't you roll your eyes at me," he ordered, "Next time that happens. I will not hold back on your punishment. You will be sore for weeks when I'm through with you."

The Doctor nodded his head, holding back the eye roll. "Yes, sir," he muttered.

The Major stared at the Doctor, crossing his arms. "Did you kill the seven men that were out there?"

The Doctor glanced at the Major and shook his head. "No. they didn't deserve to die," the Doctor stated, "They were only taking orders."

The Major growled in annoyance, glaring coldly at the Doctor. "We'll soon get rid of that stupid moral code of yours. You'll be killing at the snap of the fingers soon enough. I'll make sure of it."

The Doctor glowered. He wasn't going to kill anybody for these people. Never ever. At least he hoped. The Major pulled out some earplugs and another pair of nose clamps. He also pulled out a small box.

"The eyesight test. There will be two test for this one. One will, be testing your night vision, the other will be testing your day vision. You will be deaf and unable to smell. These earplugs are specially modified to keep out all sound. This box in my other hand." the Major held out the unrecognizable object. "Are holding contacts that will go into your eyes. They will not effect your normal vision instead recording everything from your view. We will be seeing through your eyes. We'll be able to get an idea of what your night vision is like. Is that clear?"

The Doctor nodded.

"Good. Put these in while I explain the test."

The Doctor grabbed the little box, opening it up, and placed the contacts into his eyes. They were extremely uncomfortable.

"The night vision test is similar to the smell and hearing, except you are not finding an object. We want to know what your night vision is like and how easily you can spot things in the dark without the capability of hearing or smelling. You will be attacked by different teams, as well as the automatic guns and lasers all over this building. There will also be a surprise attack" the Major explained, with a slight smirk. "This time you will have a time limit. Thirty minutes. I want to see how many hostiles you can spot and take down in this much time. If I am not happy with the number, you will be punished."

The Doctor nodded his head, quickly absorbing the information.

"This will be your last physical test. The daylight test is a lot shorter and will only record, how far you can spot something. This will be in a different room and I will explain it later."

The Doctor nodded his head, scratching the back of his neck. He was ready to get this over with. The Major stepped forward. He stuck the modified earplugs into the Doctor's ears and the nose clamp back on. The Major marched away from the Doctor.

"The Test begins now," The Major announced.

All the lights switched off and the Doctor stood in pitch black, his eyes slowly adjusting to the lack of light.

* * *

**Thank you again for all your wonderful reviews. :D So the night vision test will have its own chapter, but I will be combining the Daylight and taste test into one chapter since its more mellow. I hope you enjoyed this chapter! Thank you again for all your reviews! **


	16. Chapter 15

**Please review! I love reviews!**

Chapter 15

_All the lights switched off and the Doctor stood in pitch black, his eyes slowly adjusting to the lack of light._

The Doctor lightly tread through the room. He did not realize how much he relied on his hearing and smelling. With just his eyesight it was tough to keep track of the soldiers that were expose to attack him. His eyes had adjusted to the darkness. Thanks, to his sight being far superior to a human's. The room was a lot lighter than it would appear to a human. He may be walking through a pitch black room, but he could see everything quite clearly. It was like walking through a black and white film. Everything that was an object or person was lit up in white lighting, while everything that was space was a grayish color close to black. He searched the room looking for hostiles or what the Major claimed to be hostiles. Which very well could be hostiles, considering the men who attacked him in the last test. He just knew there were more people this time.

It was completely silent, though he wouldn't know if that were true. He had the earplugs in. There very well could be soldiers behind him or whatever the surprise attack could be. Three minutes had passed and all seemed quiet. He spun around hoping to catch a glimpse of an attacker, but no one was here. He rubbed at his eyes. The contacts the major had given him were extremely uncomfortable. They made his eyes feel dry and itchy. It wasn't pleasant. But he knew if he took them out he would be punished. The Doctor walked around one of the crates, waiting. He didn't like this situation. Yes, he could see rather well in the dark. But like how most sentient beings felt about the dark, the Doctor had similar feelings. It was not good idea to be in the Dark, deaf and unable to smell an attacker. Though, he could see, his ears and nose normally alerted him when he was being attacked from behind. At this point he felt extremely exposed.

"Oof!" the Doctor stumbled to the ground, as a rubber bullet hit him in the back. That was going to leave an ugly bruise. The Doctor quickly jumped to his feet, spinning around. His eyes caught movement of several humans all in black ops gear and night vision goggles. They hid behind the boxes, loading their guns. The Doctor jumped over to another group of crates, hiding behind them. His eyes scanned the room as he caught sight of several more human troops. Each group had at least four to five men. The Doctor quickly calculated a plan of attack. He would knock all the soldiers unconscious, hopefully, and avoid killing them. No matter how horrible these people treated him, he couldn't bring himself to murder. He knew somewhere out there most of these people had family's. He didn't want to steal their lives away even though they were quite willing to do it to others.

He watched cautiously as the men prepared their guns. One had shot him...or maybe it was one of the automatic guns. He didn't know. Five minutes had passed. Three more hits and life would get extremely miserable quite soon for the Doctor. Not that life wasn't already extremely miserable. The Doctor shook his head and watched as the men left their safe spots. He watched their mouths moving, reading their lips.

"It went this way," one of the men said. The soldier with a large gun pointed in the other direction.

"No I swear I spotted it going over there."

More of the soldiers climbed out of their safe zones all searching for the Doctor. The Doctor moved closer to the boxes, tensing. Readying himself for a fight. There were at least twenty guys in the room, all with guns and batons. Some even carried metal chains and what suspiciously looked like whips. Another soldier approached the other two soldiers, his hands gesticulating exuberantly. The Doctor read the man's lips. The soldier was talking about the Doctor and how he was able to sneak behind Parson and King and knock them out cold. Must be talking about the last test. The exuberant soldier pointed in a direction, his lips moving quickly.

"It must be hiding. Its quite good at that. Waiting for a sneak attack. Its a predator and will probably try to pull us away from the group. Picking us off one by one," the soldier exclaimed, throwing his hands in the air. The Doctor raised an eyebrow, at the animated movements of the young soldier. He couldn't hear anything, but he could read well enough. "We need to find it before it finds us!" Well, it's a little too late for that. The Doctor raised an eyebrow, sliding along the boxes his eyes never leaving the group of men. A few of them begun looking among the boxes, banging their guns aggressively against the metal crates. The Doctor glared at the soldiers, preparing himself for a quick attack. He wanted to get this over with.

The Doctor bounded out of his hiding place and the soldiers opened fire.

* * *

Subject 13 came out of no where. Many of the men opened fire immediately, but not one bullet hit the creature. It was a blur, quickly bending and twisting around each man. One of the soldiers, Douglas, ran at the alien with his baton, hoping to knock it unconscious. Douglas was a large man, much larger than the creature anyways. But the skinny alien flipped out of the way, grabbing the baton and yanking it out of Douglas's hand. Douglas fell to the ground from the force of the pull and the alien tossed the baton away. With inhuman speed, it punched another soldier in the face, quickly twirling around and kicking him in the back of the neck. The soldier fell to the floor like lead. Unconscious. Douglas ran at subject 13, his hands out, ready to wring the life out of the alien. Subject 13 stood its ground, staring evenly at Douglas. It flipped Douglas over its head, like the soldier weighed no more than a kitten. Douglas fell to the ground with a loud 'Oof', smacking his head on the metal floor. He too unconscious.

Men swung their batons and fired their guns at the alien, but none were able to shoot it. It was like Subject 13 knew exactly where to be before the bullet even fired. It bounced towards one of the men, twirling out of the way, and leaping over a fallen body. It did a round-house kick knocking out four more men, before bending backwards when another swung a metal chain. It shot up, grabbing the metal chain, and yanked it out of the man's hand. Before using the man's weight against him. The man fell to the floor unconscious. The alien sped through the men, picking them off one by one and by the looks of it, Subject 13 was far from exhausted. Another soldier ran up close, a gun in his hands. He fired at close range. Subject 13 dodged the bullet and ran at the soldier. He yanked the gun out of the man's hand and gave a scolding look.

"Didn't your mother ever teach you it isn't nice to shoot people," it exclaimed, wagging its finger like a parent would, "Shame on you! On all of you! Shooting at a helpless unarmed alien. Its just sickening." It quickly knocked the man unconscious, avoiding another bullet in the process by turning its head to the side. It quickly sped through the armed soldiers, bending and twisting. Rolling and flipping. Somersaulting. It was like watching a beautifully deadly dance that left destruction in its wake. The men frantically attacked the alien in hopes of getting a hit in, but it was impossible. The creature moved to quickly for the men to keep up.

Except one soldier got lucky. He was able to sneak around the battle and wrap his thick arms around the alien's neck. The alien gasped slightly, grabbing at the man's arms. The soldier chuckled darkly, squeezing harder. A dark look crossed subject 13's face. It growled in anger. It planted its feet into the ground and looked over at the soldier behind it.

"Nu uh," it snarled, "Its not nice to choke people, especially when you're doing it wrong." Subject 13 lifted its legs and flipped over the soldiers head. The soldiers arms bent backwards, but still wrapped around subject 13's neck. The soldier let out a hiss of pain. The creature dropped to the ground, causing the soldier to flip over the creature head and land on his stomach. The soldier groaned in pain releasing his hold on subject 13's neck. The alien bent down and pressed a finger down on the man's neck and the soldier was out cold.

It turned fiery eyes on the last few men standing, before shooting off like a blur of motion. Knocking out each man, until there was one soldier left. Jake. He had been watching the battle from afar, deciding it wiser to wait it out. After watching the creature take out Douglas, Jake knew that subject 13 was deadly and incredible. Its movements fluid like those of a warrior and Jake found himself respecting the creature more. He had heard stories from the other men about how it was a trouble maker, constantly poking at the guards. How it was a coward. But what Jake was witnessing at this moment was nothing like the stories. The creature radiated power and anyone wise enough to notice it would back away in fear. Sadly, many of the guards' egos were pumped up to the size of Russia to even register the danger subject 13 emanated. The last man fell, unconscious and Jake decided it was a better idea to run.

Jake jumped up and quickly ran to the exit. He tripped, turning around, and noticed the creature watching him. Jake stiffened, knowing that subject 13 would attack now. He closed his eyes waiting for the attack, but nothing came. He popped an eye open and the creature gave him a soft smile, nodding its head in a hello gesture. Jake waved slightly in shock. Why wasn't it attacking? Was it playing games? Subject 13 didn't move, it nodded its head towards the exit, before turning away. Jake's mouth dropped. Did it just tell him to leave? He scrambled up off the floor, staring curiously at the alien. Most of these creatures would finish them all off. But as he watched this peculiar alien, he noticed that it was checking each unconscious man's pulse. Making sure they were still alive, before giving a satisfied nod. Jake approached the alien slowly as it dragged the soldiers away from the middle of the room and over to the exit. The alien turned quickly around a fiery glare in its eyes, before the glare softened into recognition. It looked the young soldier up and down, before telling him to go. Jake nodded his head and stumbled back to the exit. He heard loud howls coming from down the hall. Gulping, he swung the door open and sprinted through them. The doors slammed shut behind him.

* * *

It had been fifteen minutes since the test had begun. The Doctor watched the young soldier escaped, before dragging the unconscious bodies, of the other soldiers, over to the side. He didn't want them to get crushed if something bigger attacked. Which he was pretty sure would happen. The Major never liked to take things lightly. The Doctor stood there, waiting. He didn't know if he had to search for the next ambush or stand here and wait for something to happen. The floor rumbled and the Doctor glanced around as the boxes and crates begun to shake from whatever was approaching.

"What in Rassilon's..." that was all the Doctor got out as a furry tank slammed into his side. He flew into the opposite wall, with a loud 'Oof' leaving his lips. He slid to the ground in pain. Cracking an eye open, he caught a glimpse of his attacker... or several. The Doctor gaped in shock. Werewolves. Four beastly ginormous Dogs that he hadn't seen since the Queen Victoria trip with Rose. Fantastic.

"Where are silver bullets when you need them," the Doctor mumbled irritably, watching the werewolves every move.

Their gray fur bristled aggressively and their furry lips curved into a snarl, showing sharp, deadly teeth meant to rip through the flesh of others. They stood at least ten to twelve feet, muscular and intimidating. Their black noses sniffed the air and their tongues smacked against their lips in hunger. Their claws were drawn and their long bushy tails wagged back and forth in anticipation. The Doctor groaned. Of course this was Major Johnson's choice, he enjoyed making the Doctor's life more difficult than it needed to be. The Doctor slowly stood up, his arms out in a calming manner. The four werewolves growled menacingly, snapping their sharp teeth together, their tail bristling in irritation.

"Well, hi there you big _scary _Doggies," the Doctor exclaimed, "What brings you here?"

The four werewolves growled and lunged forward snapping their jaws in the Doctor's direction. The Doctor spun out of the way, backing up slowly. The werewolves beady red and black eyes followed the Doctor's every step. Turning slowly around, their pawed feet smacked the ground, and the Doctor watched as they held their head up and howled angrily. They snapped their heads back in the Doctor's direction. Stalking closer and closer, teeth baring.

"How are you even in werewolf form," the Doctor questioned, not really expecting an answer. He slowly took a step back, his eyes never leaving the four werewolves. "It's not a full moon...At least I believe its not a full moon." the Doctor took another step back, quickly deducing a plan. "Besides you shouldn't even be in werewolf form, we're miles underground and you really only get affected by direct moon light..." The Doctor caught a glimpse of silver around the werewolves neck, his brain quickly coming to a plausible scenario. His brown eyes widened in realization. A smile spread across his face.

"Oh that is brilliant!" he exclaimed, "Oh, I have to give these humans some credit because those are a work of genius!" The Doctor quickly avoided a lunge from one of the werewolves and a swipe of the claws from another. Their faces contorted into a snarl of irritation, growling. "Those collars your wearing," he continued. Though he didn't need to explain anything, he wanted too. "Are making sure you stay in werewolf form. They hold enough energy in them to be the equivalent to moonlight. You can't change back into humans or whatever alien you were before. You're stuck in this form, unless someone takes the collar off or switches off the energy." The Doctor lifted a quizzical brow. "But why would this place want werewolves. Their clumsy and tend to kill everything. They have no self control. Unless these humans are just studying you guys and decided to toss you in with the poor defenseless alien." The Doctor's eyes widened. "Oh, that's just rude."

The Werewolves howled once more, though the Doctor couldn't hear it. They lunged forward, snapping their jaws. Their claws sliced through the air. The Doctor danced out of the way, avoiding each deadly snap and strike. He turned quickly around flames of anger radiating from his brown orbs. The Werewolves circled him, teeth baring and ready to rip him to shreds. The Doctor flicked his tongue out running it along his dry cracked lips. His hair stuck in every direction and his clothes were ripped to shreds. Sweat, blood, and grease coated his skin. He looked every inch a madman. Add a few werewolves and a face off he could be deemed mentally unstable. Though at this point, in his life, a psychiatric facility didn't sound that bad.

"You know what I'm going to do," he stated conversationally, "I'm going to take those collars off."

He didn't know how accurate that statement was. He'd be lucky if he got out of this without regenerating. The werewolves growled in animalistic anger. They ran forward with their jaws wide and claw out. The Doctor jumped out of the way, he spun and dodged each swing of the deadly sharp claws, hitting one in the nose. The werewolf growled in fury, swiping at the Doctor. The claws caught the Doctor on the side, throwing him back against the wall. The Doctor hit the wall with a loud bang.

He jumped back to his feet and one of the werewolf's ears perked in curiosity, before flattening threateningly. The Doctor growled back, preparing himself for a incredibly stupid feat. The other werewolves were slowly surrounding him on both sides. His eyes bounced to each werewolf, before glaring defiantly at the one with flattened ears. It was going down first.

"Alright," he snarled, " No more Mr. Nice guy." He ran forward at full speed. The three werewolves attacked him on both sides. But he flipped over them with practiced ease. The werewolves crashed into each other, falling to the ground. They got up, shook their heads, before sprinting after the Doctor. The Doctor ran at flat-ears. The werewolf growled, shooting towards him. Its arms hitting the ground with each bound and its mouth wide open showing the long deadly teeth.

The Doctor hit the werewolf, with his full strength, in the chest and the werewolf went flying into the wall. It hit the wall with a loud crack. Shaking its head, it steadily got up growling. The Doctor turned out of the way as the other three lunged at him. Eighteen minutes had passed, which was hard to believe. The three werewolves slammed into the wall with full force. Flat-ears jumped up, sprinting back over, a growl bubbling up its throat. The Doctor leapt over the charging dog, flipping over and grabbing the collar. He landed on the werewolf's furry back. Holding on tightly, the Doctor attempt to break open the metal collar. The 'wolf spun around aggressively, trying to get the Doctor off its back. The Doctor held on tighter. The other three leapt up and stalked over to the Doctor and Flat-ear, growling menacingly.

Twenty-minutes had passed. The Doctor wrapped his long fingers around the collar and yanked. The collar snapped off and the Doctor flipped off the werewolf's back as it clutched its face, howling in agony. Its body crunching and cracking as it slowly shifted into human form. It dropped to the floor, unconscious. A now naked human in its place. The Doctor jumped out of the way as the three other werewolf occupants attacked him.

He twirled and twisted and spun away from each swing, of the powerful claws and each snap of the deadly jaws. The Doctor stepped on one's tail and it howled in pain. Making room for the Doctor to jump onto its back and rip the collar from its neck. The werewolf jerked quickly as its bones sickly cracked and contorted in every direction. It too fell down, unconscious. Two more werewolves were left and five minutes to go. The Doctor continued his deadly game. Taunting the werewolves, before aiming at the metal collars around their furry necks. A few minutes left and this test would be over.

"AHHHH!' The Doctor screamed out in pain as claws dug into his shoulder. He twisted and turned, growling and howling in pain as the claws sunk in further. The Doctor let out a gurgling cry as the second werewolf came forward, sinking its claws into the Doctor's stomach, before yanking them out. Blood dribbled from the Doctor's mouth and his eyes clouded. He continued to fight back, battling off the Werewolves powerful and deadly jaws. A blood pool, slowly built around the Doctor's feet and he cried out in agony as a clawed paw sliced into his barefoot. The werewolves aggressively tearing him to shreds. The first one lifted its claws out of the Doctor's shoulder, thrusting its claws into the Doctor's back. The werewolf lifted him off the floor, the Doctor's limbs dangling and his mouth wide in a silent scream. The claws dug through his back and popped out the other end.

He couldn't give up. He didn't want to die here. Alone. So, he struggled. He fought back against the gray furred beast, reaching for the collar. He wasn't going to be defeated. He shifted his head to stare at the growling faced werewolf. With all the strength he had, he moved his hand over to the collar. Blood dripped from his mouth and back. He winced, as each pain receptor screamed in agony. He wasn't going to give up. He wrapped his long slender fingers around the collar and yanked. The Collar snapped off. The Werewolf dropped the Doctor, clutching its throat, howling. The Doctor hit the ground hard, falling into the puddle of blood, gasping as the wind was knocked out of his lungs. The werewolf screamed as its body cracked and shriveled, slowly turning back into a human. The last werewolf stood howling in rage. Slowly, circling the half conscious Doctor.

The Doctor watched the werewolf. Its steps jerky and dangerous. The Doctor groaned, slowly lifting himself off the ground. He got to his knees and shakily got to his feet, clutching his chest wound. The claws had gone through his back and out the other end. He stumbled a bit, but lifted his head in defiance. He was taking this hound down. The werewolf lunged and the Doctor slowly sidestepped it, barely missing the sharp claws. Blood pooled in his mouth, dripping down the side. His brown eyes watching the werewolf's every move. It moved jerkily, trying to intimidate him. The Doctor breathed slowly, fighting back the pain. He needed to defeat this wolf. one more minute left and it would all be over. The Doctor bounded forward, every muscle screaming in agony. He jumped at the werewolf, quickly turning away. He moved behind the giant dog and with all the determination he could muster, he leapt up onto the wolf's back. He held on tightly. The wolf spun quickly, stabbing at the Doctor. The Doctor fought back the bile that soured his throat, as he twisted his fingers into the collar. He yanked with all the strength he had left, sliding off the Werewolf's back and hitting the ground with a loud thud. The collar entwined between the Doctor's fingers and the last wolf begun to howl in pain and rage.

The Doctor breathed slowly, as the last few seconds counted down. He laid there bleeding and unable to move. He was exhausted. He saw the door snap open and three pairs of metal boots march in. the familiar face of Johnson came into view. The Doctor cracked a smile. His lips dry and reddish orange blood spilling from his slightly gaping mouth. He coughed, choking on the blood that bubbled up his throat. His eyes slid shut in pain.

"Werewolves, really," he stated halfheartedly, pain lacing his voice.

He fell into blessed unconsciousness.

* * *

**Thank you for all your reviews! :D I hope you enjoyed this chapter. It took me a while, but I think it worked out fine. I will hopefully get the next chapter out tomorrow, but I will be busy the next couple days, so it might be a slightly late update. But I'll see what happens. Thank you again for the reviews! :D**


	17. Chapter 16

**Please review! I love reviews!**

Chapter 16

_Beep beep beep..._Was the sound that caught the Doctor's ear as he slowly came back to consciousness. His eyes fluttered open and he glanced around with blurry brown eyes. _Beep beep beep..._What was that noise? He blinked a couple more times, his eyes clearing. He groaned slightly and shifted his body, a needle pinched his arm. He glanced around once more less groggy. His eyes widened in realization. He was in a medical bay. But why? He moaned as pain shot through his nerves. Oh, right werewolves. The room was bland with white-washed walls like the rest of the organization's building. He was laying on a somewhat uncomfortable medical bed. At least it was more comfortable than his bunk back in his cell. An IV was connected to his arm, feeding liquid into his bloodstream. He lifted an arm slightly, finding it wouldn't budge. Glancing over, he noticed he was chained to the bed with iron cuffs, connected to a long metal chain, attached to the bed. The chain allowed him to move his arms over to his chest, but no further then that. The Doctor sighed in despair. He was wearing an oxygen mask and quite a few wires were attached to him. He spotted the source of the beeping when he turned his head to the side. A heart monitor. The Doctor sighed heavily, continuing his self-evaluation. Apparently, he had gone into a healing coma because many of the wounds that he had gained were semi-healed, which only left a dull pain throughout his body. He wasn't wearing any clothes, except for a pair of boxers. At least they allowed him some dignity, but other than that he was fine. His torso and shoulder was wrapped in thick gauze, as well as his foot. He could safely assume that he wasn't going to die and regenerate. He was extremely lucky to get out of that test whole.

The sharp clips of metal boots approached the door on the far right. The Doctor turned his head to catch sight of the scowling faced Major Johnson. His blonde hair neat and tamed and his light brown eyes cold. His arms were behind his back and as always, he carried the air of authority.

"You're awake," he stated coldly. Marching over to the Doctor's bedside. "About time."

The Doctor groaned as he focused on the Major, a headache already pounding between his eyes. The Major stood stiffly, slowly scrutinizing the Doctor.

"Sorry if I held your plans back," the Doctor retorted sarcastically, his voice hoarse. "Getting ripped apart by werewolves does that to a guy."

The Major sneered at the bedridden Doctor. He reached for the baton, at his hip, before thinking better of it. Dropping his arms, they rested stiffly at his side. The Doctor glared back at the Major, wincing slightly as he jostled his wounded foot.

"Guess you can't win them all," Johnson stated indifferently. The Doctor's mouth gaped. The man was completely psychotic. He was almost ripped to shreds by four extremely, large werewolves and the Major didn't even care. The Doctor's blood boiled with fury. How could these people treat him this way?

"For your information," the Doctor bit back icily. He felt the storm brewing inside of him. Which wasn't a bad idea unleashing it, except at this point he had no idea what devastating effects it would have on his already abused body. He didn't want to take his chances. "I did defeat every test you put me through. I even fought those stupid werewolves of yours. Injured and bleeding! Plus came out of this whole ordeal alive. I think I can safely say I won." The Doctor leaned back against the thin pillow, holding back a moan from bumping his back a little to hard. He crossed his arms petulantly and glared at the Major. The Major sneered, his top lip lifting slightly. His hands twitched with anticipation, ready to throw a punch.

"You let one man escape," the Major growled, "and didn't kill one person or creature that I sent into that room. You also ended up in the medical wing." Johnson glanced the Doctor up and down with disappointment. The Doctor's eyes slitted dangerously. He felt his hand shake with suppressed anger and resentment. "I am not impressed and this is going to cost you," Major Johnson concluded. He crossed his arms behind his back in an authoritative manner.

The Doctor gritted his teeth. "They didn't deserve to die," he stated, "I am not going to kill anyone in cold blood. Human, werewolf, or some other species. It is wrong."

"That's not what it said in your file," Major Johnson retorted. The Doctor felt his hearts twist in pain from the cruel jab. He gulped, trying to release the emotional lump in his throat. "Whole worlds. Whole Civilizations and you murdered them all. Wiped out entire species," the Major hissed, pacing the room. He smirked at the reaction that the Doctor gave. The Doctor buried his face into the pillow. "So why aren't you willing to kill for us?" The Major bent low, getting into the Doctor's face. "I blame it on stubbornness, pride, and arrogance. That is why I won't let you get away with anything."

The Doctor glanced up at the major. The muscles in his throat tightened as he felt raw emotions bubble. He threw up a mask, unwilling to let the major witness the pain his words had caused.

"T-there's a reason behind all that destruction," the Doctor stuttered, swallowing loudly. "It had to happen." The Major faced the Doctor, a sneer ever present on his face. He glanced the Doctor up and down, his expression disgusted. The Doctor shrunk back into the bed. He felt like scum on the bottom of someone's shoe and that's probably what he was. What was so important about him anyways? He was just the universe's scapegoat. Nothing good ever happened to him, everyone always left or died and Donna would soon follow.

"There's a good reason behind what we're doing as well," the Major stated, "I am not pleased with you subject 13. If you're not going to step up your game I will be forced to use brutal measures. I have been very lenient with you and my punishments mild. But if you don't shape up and except this as your new life..."the Major glared coldly. "I can make your life extremely ugly."

The Doctor didn't respond. How could you respond to a threat like that? He just needed to get out of here. "You're losing your relaxation privilege for a few days. You will be training with me night and day, 24/7. Oh, we mustn't forget your time with the scientist," The Major stated. The cold look never once leaving his face. The Doctor sighed and slumped. His brown eyes growing foggy with depression. "You will also be losing your food and water privileges for a day or two because of that mess up during the night vision test." The Major begun pacing once more, back and forth, before pausing and facing the Doctor. "You better rest up because I expect you out of that bed in the next couple of hours. We have two more test to finish up and training the rest of the day." The Doctor stared at the man in shock. Was Major Johnson unable to see the bandages wrapped around his torso or the heart monitor beeping next to him? The Doctor flushed with anger, grinding his teeth.

"But I'm injured," the Doctor exclaimed, "I got into a fight with four werewolves, who were quite pleased to rip me into shreds." The Major glared at him icily, his lips curving into a frown. He turned quickly on his boot, before marching towards the door. He glanced back at the Doctor.

"So," he responded, his lips still shaped into an ugly frown, "not my problem. You should have been more aware. This is your fault and a lesson you must learn. I am not going to halt the schedule because you're injured." the Major opened the door, placing a foot out. "In two hours I will be coming back to collect you. Understood?"

The Doctor nodded his head. "Yes,Sir." His eyes were watching his fingers tug at a small string. He couldn't look at the Major. His face had turned a bright red that reached the tips of his ears. He felt angry and humiliated. The more he thought about the situation he was in, the more he wanted to kill the man in front of him. But he could not. It was against his morals and it would only prove to these xenophobic, sadistic creeps that he was nothing more than an animal. He took several deep breaths, calming his nerves. He tugged at the blanket a little more, wringing it between his tense fingers.

"Good," the Major replied. He watched the Doctor and smirked at the redness of his face. "Get some rest," he ordered, "Or go into that healing coma thing. I want you fresh and awake for the next two test. I don't want another mistake." The Major marched out the door, slamming it shut behind him. The Doctor glared at the closed door, before attempting to find a comfortable position to sleep in. His face flushed with fury. He closed his eyes, falling into a much needed healing coma. He wanted to fix as many wounds as he could, before the major returned to drag him off to the next set of tests.

* * *

**Thank you for reviewing! I realize this is not the testing chapter I planned on writing and it's rather short, but I needed an inbetweeny chapter after the last one. I hope you enjoyed it and I'll try to get the next one out tomorrow. I'm getting my drivers permit and that will probably eat up my day, thanks to the long wait. :) But I'll see what happens. Again thank you for the reviews. :D**


	18. Chapter 17

**Please review! I love reviews!**

Chapter 17

The Doctor woke to the loud jingle of chains as somebody unhooked him from the bed. One brown eye popped open to the sight of a medical physician and Major Johnson. Had two hours already passed? The Doctor groaned, stretching slightly as the chains were snapped off his wrist. The pain had died down quite a bit. It was now just a sore throb in his torso and shoulder. His healing coma had fixed a lot of the wounds and he could now move around without the sharp sting of agony. The chains slid off and he was yanked off the bed and to his feet. The wires, heart monitor, and IV already removed. The Doctor stumbled into the arms of Major Johnson, groaning from the rough treatment he was given. He glanced up at the Major, before straightening himself up. He backed up slightly, clutching his stomach. The Major looked him over thoroughly. A cold frown present on his face. The medical physician stepped forward, unraveling the gauze. The Doctor winced from each yank and a trail of bloody bandages were soon at his feet in a neat pile. The physician bent down and prodded the Doctor's wounds, checking how far they had healed. He turned his gaze away from the Major and physician, blushing modestly. He didn't like being poked at even if it was just his wounds. The medical physician nodded her head in affirmation. She stood up and strode over to the cabinets, pulling out a package of white gauze.

"It seems subject 13 has healed up quite nicely," she explained, "The healing coma, it went into earlier today, had stopped the bleeding and healed up many of the wounds." She unraveled the fresh gauze and begun wrapping it around the Doctor's torso. The Major slightly bobbed his head, showing that he was listening. "Many of the shallower wounds have healed, including the foot and shoulder wound. They have nicely scarred over since the last time I checked the alien. My main concern is the wound in its stomach and the impaling that went through its back and out its chest. The stomach wound was leaking stomach acid when we first received it. We cleaned it up but I feel like its a good idea to keep an eye on it. Make sure subject 13 doesn't get any infections. I have antibiotics set up for it just in case something goes wrong and the healing process slows down. Overall, its healed up quite nicely. Its also standing up fine which is a good sign. So I don't have any disbelief that it won't make a full recovery." The technician wrapped the last bit around the Doctor's torso, before taping it together, and giving it a light pat. The Doctor winced slightly from the hand pressure, running his hand gently along the now bandaged wound. The technician stood up, stretching slightly. She picked up the old gauze and threw it away. Washing her hands, she listened intently to the shallow breathing of the Doctor, worried about his health.

"What do you suggest I do about its training and testing," the Major stonily asked, "I can't stop training it. What is your professional advice?" The Major glared impassively at the Doctor. The Doctor was leaning slightly against the bed, weariness taking over his body. He groaned slightly as a dizzy spell hit him, he just wanted to lay back down.

"I suggest you take it easy," the physician responded, "Don't necessarily stop your training, but give it breaks when subject 13 needs them. Pushing it to hard will only hurt your goal. Same goes with the tests, the scientist will inflict on it. I would prefer it to relax and sleep, but we can't stop its training as you had said." Major Johnson nodded his head, before massaging his temples. He felt the bite of a headache coming on.

"What about today's test. The vision and taste testing. Can we still perform these last two test today?" The Major glanced over at the Doctor, who was now slumping against the bed. His knees had given out after standing up for too long. The physician noticed this. She made a quick evaluation before turning her gaze back at the Major.

"As long as those two test are not physically tiring, they will be fine. I prefer if subject 13 wasn't standing for long periods of time, sitting would probably be best considering its lack of energy." The Major nodded his head, grinding his teeth. This was not what he needed. He marched over to the Doctor, who had his eyes closed, and yanked him up from the slumped position on the bed. The Doctor opened his eyes startled from the sudden rough movement. He was exhausted and all he wanted to do was sleep. But it seemed that 'privilege' was denied to him. He was dragged to the middle of the room and fresh clothes were tossed over to him.

"Get dress," the Major ordered. His arms crossed and eyes squinting coldly. " You have two more test to perform and training with me afterwords." The physician rolled her eyes. It seemed the Major didn't heed her warning. He was going to work that poor alien to death if he kept it up like this. But she wasn't the one in charge, so she shrugged her shoulders and didn't say a thing.

The Doctor stumbled into the new pair of pants. He felt like lead swimming through a pool of molasses. He pulled the shirt on over his head. His head popped out exposing tousled unruly hair. The Major watched him impatiently as he dressed, his foot tapping and fingers drumming against his arm. He yanked the Doctor away as soon as he was finished, marching him out the door.

* * *

The test was simple, all the Doctor had to do was stand at the end of a long room and stare at stuff, describing the object in precise details. He wasn't wearing the earplugs or nose clutches again since he was just staring at things and people were calculating the distance he could see. It was rather peaceful considering the last few test he was forced to do. The room was strange, it started off small but as time went by the back wall begun to move backwards. Every time he described something the wall moved back another 10 feet and he was given another tiny item to describe.

The Scientists and Major stood at his side watching the process and quickly jotting down notes each time he explained something. The wall was at least a good three miles away it was a very strange room, but apparently it was useful to use if they didn't want him outside. Dr. Carter and Black stood next to each other, they were quickly discussing their findings with extreme enthusiasm, well at least Dr. Carter was. Dr. Black was more on the quiet and cold side of the conversation, taking everything in with professionalism.

The Doctor rubbed his stomach once more. The Gauze was extremely uncomfortable and itchy, but he had to wear it if he didn't want his insides to spill out allover the floor. The wall moved back another ten feet. The Doctor allowed his mind to wander. He thought about the escape plan, the tool that was barely finished, he had to work on that quicker, and Donna. He worried about Donna the most. He wanted her out of here as soon as possible. He didn't know what happened to her when he wasn't there. He knew fully well that she could take care of herself. She was tough, independent and would never let anyone take advantage of her. But he still worried. The guards could hurt her without him ever knowing. She was to proud to tell anyone when she was hurting which was very similar to himself. A soft smile graced his lips. She was a lot like him, very proud and stubborn. He shook his head. He didn't need to worry about Donna. She was probably fine, making friends with the other prisoners and getting to know them. She was brilliant. She had figured out his escape plan without him even needing to explain it to her. Knowing Donna, she was probably figuring out the routine of this place. When the guards came for the prisoners, what time supper came along, and other important little scheduled routines that only she would notice the details too. _Smack!_ The Doctor was brutally awakened from his musing. A baton had caught him in the arm and he slightly groaned, massaging his now bruised bicep. He turned around to face the icy stare of Major Johnson. The man just couldn't give him a break.

"Are you deaf or something," the Major growled, twirling his baton menacingly. Dr. Carter and Black glanced up from their research, to watch the confrontation. Dr. Carter had a slight smirk on his face. His black eyes squinted observantly. The Doctor glared at the three people.

"No," the Doctor replied, "I am not deaf. Which you should know after spending twenty nine minutes and thirty seconds watching me stumble about during that hearing test." The Major snorted in distaste, his eyes squinting darkly. The Doctor turned away from the Major and looked at the far wall of the long room. At the end of the room was a weird box shape item. The Doctor extended his eyesight slightly, so the box became clearer. He smiled. "Its a brown box, as all of you may have seen," he responded. The Major's scowl grew darker. "But there are a few dents and holes in the box. Looks like somebody kicked it and than stabbed it with a pencil. There's also a few drawings, mostly scribbles and stick people. Terrible artist to whoever drew on that box. Looks like a two year old got hold of a blue and pink marker. There are a few black lines on the box and writing. If you want me to read the writing out loud I can. Its in small print. Basically says 'Made in China.' Why is everything made in China these days?" The Doctor quirked a curious eyebrow and glanced over at the scientist. "How was that?" A cheeky smirk twitched at his lips.

"Incredible," Dr. Carter exclaimed, turning towards Dr. Black, "It seems to be able to extend its vision. Seeing farther than any human is capable of also noticing exact details." He quickly flipped through his notes. "I'd like to see how far his sight can extend. So far it can see perfectly clear at three miles. I say we keep going until its vision starts to blur." Dr. Black nodded her head in agreement. Her blue eyes glanced over her glasses, observing the alien.

"Move it back another ten feet," she responded,"It has proven to have acute eyesight similar to that of a hawk's." Dr. Carter smirked his agreement, before turning to one of the technicians, waving his hand in a gesture of move it back another 10 feet. The wall moved back farther and a tinier item was put up against the wall. "Continue," Dr. Carter ordered. The Doctor did just that.

* * *

"Subject 13 is an absolutely remarkable creature," Dr. Carter mused after the ending of the test, "It was capable of spotting something clearly five miles away." Dr. Black nodded her head, her short brown hair bouncing slightly with the nod. A stony, cold expression on her face. She quickly flipped through the notes, impassive eyes scanning over data. She sighed heavily, taking off her glasses and rubbing her strained eyes.

"Yes," she agreed, "Quite remarkable. Though it seemed to struggle once its passed that five mile marking. It missed certain details. I wonder how subject 13 controls it because I am sure it would be completely overwhelmed if it was capable of seeing that much 24/7." Dr. Carter nodded his head, scratching his chin.

"From what I have studied and learned about this alien's physiology. It is capable of controlling many of its body functions, as well as having them work automatically. I think it can decide when it is in need of a certain body function and can regulate it. I have seen it slow down its hearts beats when there is to much strain and I am pretty sure it turned on that bypass system during the suffocation test. I feel like the same goes for its senses. It probably can make each sense more acute when it needs too." Dr. Black quickly jotted down the new hypothesis, turning a few pages, she stopped on a blank page.

"The next test is the taste test, correct," She questioned. Dr. Carter nodded his head, licking his lips.

"Quite," He responded, " Major Johnson has already taken subject 13 down to the lab where we will proceed with the test. I am curious what this creature is capable of. We're going to blindfold it and plug its nose, so it can't see or smell the item. Its going to tell us the ingredients of the item or what the thing is. It will be fascinating to see what this creature can distinguish using its taste buds."

"It will definitely make a great assassin when we're through," Dr. Black stated, her eyes for the first time expressing excitement, "Imagine a creature that moves that quickly and can pinpoint a target five miles away. Plus with its healing factor and other odd bits in its physiology, it would be unbeatable." she turned quickly towards Dr. Carter, a matching dark grin crawling across her face. "The Underground could destroy their enemies with ease. Oh, yes, subject 13 will make an excellent asset to the program. We can also rent out its uses to other agencies or wealthy businessmen or whoever may need its service and has money to pay for it. This will bring a little more income to our agency."

Dr. Carter's grin stretched, with all the possibilities racing through his mind. "We should bring this up with Colonel Graham. I don't think he has thought about renting out Subject 13 to other groups yet. It will help build an alliance basis between us and other agencies. Of course we will still have room for testing, but if we can use subject 13's full potential, I think we can soon be at the top."

Dr. Black nodded enthusiastically, her tongue poking out in thought. "We just have to rid that rebellious attitude."

"That is what Major Johnson is here for, my dear,"Carter responded. Dr. Black smiled a crooked grin. They had a plan and they were going to make sure they enforced it. They strode out the door and towards the next lab, where the Major and alien were waiting for the next test to begin.

* * *

The Doctor was sitting in a seat this time, blindfolded and plugged up again. He was getting really sick of being blinded and unable to smell. He sighed as he heard a bowl placed in front of him.

"Subject 13 tell me what this is," the Major ordered. He heard the rustling of papers as Dr. Carter and Dr. Black stepped forward eagerly to hear the answer. He had been at this for a good twenty minutes and he was sick of tasting things. Everything had been nasty or uneatable. Even if it was eatable he wouldn't of eaten it anyways. They might of laced it with poison.

His chest and back begun itching intolerably again. He hated being injured. It was always either excruciatingly painful or intolerably itchy. He sighed, picking up the container and taking a lick. All he wanted to do was go back to his cell and sleep for a millennium. But no, Major Johnson wasn't happy with his performance during the night vision test because he got ripped to shred by werewolves. Now he was going to be punished with extra training for his failure. It just wasn't fair. The Doctor's nose crinkled with distaste and he wagged his tongue in disgust. Blood. They had given him blood. What do they assume he was? A plasmavore. He heard a grunt behind him and decided it was best to explain the substance.

"It's blood," he stated still grimacing, "Type A. Low in iron though. Whoever's blood you took, you should really advise them to take an iron tablet everyday."

"Good," Dr. Carter said, "That is correct." the Doctor heard the metallic bowl slide away and a new one placed in front of him. He rubbed the smudge of blood from his lip. "Try this one." the Doctor picked up the bowl, taking a lick and smacking his lips together. This time it was something fishy with a hint of mint. Not the best taste in the world. "Fish oil. More specifically cod fish oil. It has a minty taste to it too. Like you crushed mint leaf and mixed it together. It also taste rather salty. Ocean salt? Must be."

Dr. Carter nodded his head impressed. Dr. Black watched with fascination as the Doctor pinpointed each taste without any hesitation. Quickly marking down each answer he got correct. The Doctor listened to the pen running along paper rapidly.

"Very good," Dr. Carter stated. He pulled the bowl away and placed something metal in front of the Doctor. "Tell me what metal this is." The Doctor picked up the metal tube and licked it, he shrugged indifferently. "Copper. Or if you want to be specific, the periodic name for copper is Cu. It has an atomic number of 29 which is the number of electrons and protons and the atomic mass of 63.55 in AMU. Also I tasted the salty taste of sweat from someone's hand who brought it over. The taste is familiar to something I have smelled before. One of the technicians maybe. They might want to clean their hands better. I tasted a bit of dirt, which is never nice when mixed with sweat."

Dr. Carter smiled. "Incredible." he removed the copper tube from the Doctor's presence. He looked over and noticed one of the technicians staring sheepishly at his hands, rubbing them together. The hands were slightly tinged with sweat and dirt which wasn't at all professional. "I'll let him know," he responded. He turned to Dr. Black and raised an eyebrow. She nodded impassively, but the sparkle in her eyes destroyed the cold demeanor. "Shall we continue," Dr. Carter asked rhetorically. Placing a new item in the Doctor's reach. The Doctor nodded his head, picking up the new item, and licking it.

* * *

Thirty minutes later:

Major Johnson had taken subject 13 away, for training, after the test ended. It was limping slightly which did not escape the professional eyes of Dr. Carter and Dr. Black. They stared at each other an identical dark grin growing on both their faces.

"Yes, I believe we have found our perfect weapon," Dr. Carter stated knowingly. Dr. Black nodded her head enthusiastically.

"Colonel Graham will be pleased to hear about our discoveries." Dr. Black turned on her high-heeled shoe and marched out of the lab towards her office, jotting down a plan for the test she would soon be performing on subject 13.

* * *

In Colonel Graham's office, the Colonel was slumped in his chair. His eyes moved rapidly back and forth, his mouth gaping open. His fingers loosened and a soft ping was heard as a needle hits the ground. The colonel opens his mouth widely. A loud gasp echoes throughout the room. His fingers twitch sporadically and drool slid down his chin. _Crack!_ fingers snapped in half. The sound swiftly bounces off the soundproof walls.

* * *

**Thank you so much for all your encouraging reviews. I get so excited when I see a new one posted. :) I hope this chapter was satisfying to you all, it took me a couple days to write because of the drivers knowledge test I took yesterday. I can proudly say that I passed and now have my permit. :D It was a great day and I even got to practice a bit. Thank you again for the reviews and I will hopefully get the next chapter out tomorrow. :D**


	19. Chapter 18

**Hi, thank you for all your reviews. They are wonderful and extremely encouraging. :) So, this chapter will actually have mostly Donna and not very much Doctor. It is basically what she did the few days the Doctor didn't return to the cells. I plan on balancing Donna and Doctor time as much as I can. I hope you enjoy this chapter! :D Please review! I love reviews. :)**

Chapter 18

Donna Noble hadn't seen the Doctor in quite a while. They had dragged him off, she calculated at least a few days ago, and taken him to God knows where. She had taken it upon herself to work out the escape plan and see which alien prisoners were willing to help. Though many were completely terrified to escape and had no faith in the Doctor's ability at the moment. She had made quite a few friends during his absents and learned quite a bit about their species. What their abilities were and how come they ended up in this cell block.

Apparently, this cell block held all the aliens that they considered to be dangerous and violent, but not yet trained. There were several other cell blocks as well, that held other different beings. There was a testing block where all the aliens who were mainly used for experiments and research were kept, a poisons/ virus cell block where all the aliens who gave off poisonous and viral gasses were stored, and a supernatural block. Each block had about two to three hallways worth of cells. According to Ama, the young alien who was the most friendly towards her, there was another cellblock for trained aliens who were expert killers. This was the cell block that the Doctor would most likely be sent too once they finished training him.

Donna talked to and learned about her fellow prisoners, since the Doctor was barely here to do it himself. She had learned that Ama, who was a Shian as the Doctor had explained early, was a powerful telepath. She could pick the thoughts from someone's mind miles away. She explained that her species were master manipulators. They could control a simple mind, with the snap of the fingers, making them do whatever they want. The only reason she could not escape was that these humans were using a alien technology to control her telepathy. They had placed a metal pad against the back of her ear. The pad shocked her every time she tried or even thought of using her telepathy. It apparently had tentacles that dug into her skin and hooked into her skull.

Another alien that had deemed himself useful was Roctarus,who was from the planet Petra. At the moment he was in humanoid form, the only thing that made him look different was that his body was made out of soft grayish brown rocky skin that gave him the appearance of a walking, talking rock. But what was deadly about Roctarus was his ability to transform into a fifteen foot rock monster. When he was in this form he is completely indestructible and incredibly strong. Nothing could penetrate his rocky skin. Part of the reason why he wore a metal collar around his neck that made his ability dormant.

There were many other aliens in this cell that wanted to help as well. A fire breather, another who had gills, the groske who was actually extremely strong for its height, a young alien with beautiful black wings, and many others all with unique strengths.

They had all agreed to help with the escape planning, though they were still skeptical. They explained to Donna what the daily schedule was, something Donna had noticed quite often. They woke the prisoners up by turning on the lights, the guards come by throughout the day except when it was the supposed lunchtime for them, the aliens who were brought to the labs or training area were sent back to their cells, the cook came along afterwords, and all lights were turned off for five hours. So the aliens could sleep before the cycle repeated itself. But most times, not every alien was in their designated cell block during the supper and resting time because sometimes the scientists or trainer wanted extra time with them.

Donna leaned back against the far wall of her cell. Her legs were brought up against her chest and her chin rested on top of her knees. Her red hair curtained her face, blocking it from view. She was organizing her plan of escape and thinking of the best way to explain it to the Doctor.

_Bang. _Donna shot her head up at the sound of the large metal doors banging open. The loud clips of feet hitting the metal ground echoed off the walls. She stumbled to her feet, hoping the Doctor was back. She was worried about him. Sadly, it was just a lone guard. He was young with a boyish face and tousled sandy blonde hair. His green eyes darted back and forth, searching for someone. He chewed on his lips nervously, which was quite strange considering he was a guard and everything. It was almost like he was nervous about talking to another being. He shook his head and straightened himself out. Clearing his throat, he glanced at all the occupants in the cell block.

"Has subject 13 come back to its cell yet," he asked confidently. Donna's eyebrows shot up to her hairline. What did he want with Spaceman. "I just want to ask it a few questions." The man looked desperate, like somebody trying to find answers. Donna couldn't help but feel a little sorry for him. She understood his position if he recently talked to the Doctor. She had the same feeling after her first adventure with the crazy martian.

"He's not here at the moment,"she stated, "He hasn't been here for at least a few days." The young man turned towards her. Shocked that someone actually answered him. He walked cautiously over.

"Hi," he greeted. His green eyes dancing with curiosity, "You don't look like an alien. Are you the same species as subject 13?" Donna's eyes narrowed dangerously, she despised the code number that the Doctor was given. She thought it wrong and demeaning.

"Oi, He is not an it and he has a name. Got it Sunshine,"Donna acidly stated. The young guard nodded his head, startled from the brash tone. "As for your other question. I am not the same species as that crazy martian. I'm human."

"You're human," the guard asked, running his fingers through his hair. "But we don't keep humans here..."

"Then why am I here,"Donna retorted, sarcasm dripping from her lips. She knew she was being a little harsh, but she was irritated and if shouting at the young guard would make her feel better than she would shout to her heart's desire. "Oh yeah, I forgot! They brought me along to keep spaceman compliant. I wonder how that's working for them?" The young guard quickly bobbed his head, eyes wide and fingers twitching nervously. Apparently he had never been yelled at by an angry ginger before.

"I guess you know subject 13...I mean." The guard glanced over at her for help. Donna rolled her eyes.

"The Doctor."

"I guess you know the Doctor pretty well than," he concluded. He lifted an eyebrow curiously. "Are you two a couple." Donna scoffed, rolling her eyes. Even without him here, people believed they were a couple.

"No, I am not married or dating skinny boy," she exclaimed exasperated, "Why does everyone always assume we're together. We're just friends. Best friends. That's it. Does that answer your question." The guard nodded his head, startled by the reaction.

"Good, I have a question for you than," Donna stated, her blue eyes narrowing suspiciously. "Who are you and why are you so curious about the Doctor?" The guard rubbed the back of his neck uncomfortably, turning his gaze back at Donna. "Name's Jake and the Doctor spared my life." Donna's eyebrows shot up.

"What?" she exclaimed, startled by the revelation.

* * *

Jake told his story. About the night vision test and the way that the Doctor fought off all those men. He explained he didn't want to fight after seeing the Doctor take down one of the biggest guys in the group and how he hid away, waiting for the fight to be over. The Doctor had spotted him and let him go.

"It was a cowards move I realize." Jake sighed. "I should have been with my team. But...I didn't see the point in the fight. After the short battle was over, I ran and he let me go." Donna sat against the wall, listening to the tale. She had no idea that the Doctor could be that dangerous. He'd always been her mad Spaceman. But she should have known he could be deadly if he wanted to. Think about the Racnoss. She sighed, clasping her hands together.

"Was he hurt?" Donna glanced over at the young guard. He quickly shook his head, an amused smile playing at his lips.

"No, not that I know of anyways. I think what was mostly hurt was the mens' pride after being destroyed by the skinny alien. Especially some of the bigger men who were taken down first."

Donna laughed. "Of course. My main surprise is that he actually fought."

Jake raised a brow. "Does he normally not fight? Because he seemed to be an expert."

Donna shrugged, waving her hand dismissively. "He's normally a pacifist, using words instead of his fists. But who knows what skinny boy's picked up in his 900 odd years."

"900 years?" Jake's voice hitched slightly from shock, "He looks 30 or something."

Donna shrugged again, picking at her nails."He lives longer than humans. He behaves like such a stubborn old man sometimes and yet so childish and full of energy. Everyday is an adventure with him. I don't believe I have had one day when we weren't running for our lives or captured by some evil megalomaniac."

Jake shook his head. "Unbelievable,"he whispered. His eyes shot back over towards Donna. "What is it like traveling with him? More out of curiosity really. I just never really talked to aliens before. Which is weird, considering where I work."

Donna rolled her eyes and laughed. "Like traveling with anyone else. We have fun, get on each others nerves, make up by the end. No difference. Except he can do really weird alieny things at times, but that's just him." Jake bobbed his head, leaning back slightly. A sharp ring was sounded from his pocket. He reached in and pulled out some type of high tech cellphone, before pocketing it once more. He got up from the ground and brushed himself off.

"I've got to go," He explained quickly, "Nice meeting you. I want to talk to the Doctor at some point, so I'll be back later. See ya." Jake quickly marched down the hallways and out the door. Donna waved. Rolling her eyes, a soft smirk twitched at her lip. Hopefully she had just made an ally. Having a guard on their side would be really helpful to their escape.

* * *

"You see, Colonel," Dr. Carter explained, a sickly sweet smile on his face. "I think mine and Dr. Black's plan about renting out the creature after its fully trained is an excellent idea. It will bring in more income for our agency and build a better alliance system for us if we shared the alien."

Dr. Black nodded her head in agreement. She pushed a strand of brown hair behind her ear, pursing her lips. She watched Colonel Graham's reaction intently. The Colonel was frowning, though he was always frowning. It was normally the only expression he knew how to present. The Colonel was wearing dark sunglasses over his eyes, so Black was unable to see his actual reaction. Why didn't he just take the sunglasses off. It wasn't that bright in his office.

Graham's hands were underneath the desk. A slow tap had started,before switching into a scraping noises. It sounded like claws were scratching the bottom of the desk. The Colonel leaned back, listening to Carter's plan. He glanced over at Dr. Black, who stared at him suspiciously, before her gaze turned indifferent once more.

"The alien is absolutely incredible," Carter exclaimed. The Colonel turned his head back over to the creepy scientist. "It can hold its breath for a long time and from our recent tests it has proven to be extremely strong, quick, and flexible. It's senses are off the charts. Nothing I have ever seen before. I know we're trying to find the perfect fighting machine and I think I found it. The ultimate assassin."

The Colonel grunted. Dr. Carter reflected off his dark sunglasses. "Never give an alien a human's job. They're not to be trusted. Backstabbing freaks," The Colonel snarled. Dr. Carter was slightly taken aback by the harsh words.

"But Colonel Graham,"Dr. Carter responded, "Part of the reason why we have project emerald is to build the perfect weapon using non-humans. So, they can train and do the dirty work that most humans don't want to do. They are tools. Nothing more. You said so yourself." The Colonel eerily watched Carter. His lips showing no emotion. Dr. Black's eyebrow twitched in curiosity. She leaned forward and stared the Colonel down.

"Are you feeling alright, Colonel," She asked, "You seem to be slightly forgetful." The Colonel whipped around to face Dr. Black.

"I'm fine," he growled. He turned back to Carter. "I like your idea, Renting the creature out. These aliens are nothing more than tools. Tools that need to learn who's in charge. Keep running test on subject 13. I want to know as much about this creature as possible."

"So, you will consider our idea," Dr. Black asked stonily. The Colonel nodded his head, massaging his temple with his fingers and wincing slightly. He was wearing black leather gloves as well.

"Leave," he ordered. He picked up a gray file, flipping it open. Dr. Black and Dr. Carter glanced at each other, before turning away and striding out the door. They slammed the door shut and the Colonel glanced up slightly. His gaze lingered on the closed door. His teeth gritted in pain, as a new spasm took over his body. Coughing slightly, he turned back to the file. The file was titled Donna Noble.

"Well, Well. Seems that you're a bit out of your designated year Ms. Noble," he stated, "Seems to happen when you're traveling through time. Not a huge hop, but a good seven years or so at least." He put down the file. He needed to talk to Ms. Noble and see how much she knew about the Time Lord. A small smirk crossed his face. She might be useful to the agency and their goals after all.

* * *

**I hope you enjoyed the chapter. :) More plot building. Thank you again for all your reviews. More will be revealed later. :)**


	20. Chapter 19

**If you have noticed I had to change the projects name from project Indigo to project emerald. Apparently UNIT during Journey's End called the teleportation device project Indigo. And here I thought I was being really clever :)I want to thank Cjabbott98 for pointing it out. So, Thank you and I hope you all enjoy the next chapter. Please Review! I love reviews!**

Chapter 19

"My turn Doctor?" the innocent voice of Bobby asked. A checkerboard was setup outside the Doctor's cell. Bobby was cross legged on the floor, holding one of the red checker pieces. His tongue slightly poked out at the corner of his mouth. He glanced up at the Doctor with respect and admiration in his eyes. The Doctor was one of his first and true friends he ever had. Most people normally agreed to be his friend but never really acted upon it. But the Doctor and Donna excepted him for who he was and were willing to play any games he wanted. He was happy to help them escape. Even though it meant that he would never see them again. They didn't deserve to be in a place like this where they ate parasite-infested birds and mud.

Bobby had visited the cell block several times, in the last few days, with hopes of spotting the Doctor here. But the Doctor had not been there for four days straight at least. So,Bobby spent time with Donna. They talked and played games and Donna taught him games he never heard of before. She told him she was worried about the Doctor. He had been gone for a long time. Bobby was worried too.

Until, this morning when he returned back for a visit. He found the Doctor laying on a cot, resting. Donna was fussing over him in the cell across. He looked extremely tired and sore and Bobby didn't want to disturb him. But the Doctor had snapped his eyes open and welcomed Bobby with a huge grin. Since then they had been playing checkers. The Doctor had only won once while Bobby had won several times. It seemed the Doctor's mind wasn't really in the game today.

"Yep," The Doctor responded popping the p. He leaned against his cell, holding a giant, metal monstrosity. Wires were sticking out at different angles and metal was smashed and twisted in different place. The Doctor's dark brown hair was sticking in every possible direction, giving him the appearance of a mad scientist. He held a screwdriver in his hand as he twisted a screw out, destroying the cellphone he had gotten his hands on. Bobby moved his piece up, pushing his glasses up his nose, with a proud smile on his lips. The Doctor seemed extremely focused on the metal contraption, that looked more hazardous than helpful. Bobby lifted an inquiring brow, staring at the Doctor curiously.

"How is that thing going to help you," Bobby asked, "It looks unsafe." The Doctor glanced up at Bobby, his tongue poking out between his teeth slightly and his brown eyes wide. He separated several of the items into different piles, picking up another wire. "If I can get it to work properly, it should be able to cancel out the surveillance cameras turning them temporarily off. I'm adding in a few other doohickeys that will also cause the energy fields to malfunction. Releasing everyone from their cells."

Bobby nodded his head not completely understanding how a metal massacre, like the one in the Doctor's hands, could do something like that. But he would have to trust the Doctor's judgment. He seemed to know what he is doing. "Its your turn Doctor." The Doctor glanced up from his invention, as Bobby slid the checkerboard underneath the energy forcefield. The Doctor's eyes danced over the board, before moving a piece, and sliding it back to Bobby. Bobby sighed.

"I wish I could come with you, Doctor," He stated, "I would love to see the stars." The Doctor glanced up, a soft smile spread across his face.

"Maybe you can," Donna exclaimed, overhearing the conversation. "It would be nice having you along." Bobby looked expectantly at the Doctor. A hopeful grin on his face. The Doctor nodded his head in agreement, slightly wincing from the sudden jerk. A smile spread across Bobby's face.

"Oh Boy, Doctor. Can I really come," Bobby asked. The Doctor nodded his head a little more enthusiastically adding a 'yep' for good measures. "I won't let you down Doctor...and Donna. I am really good at cleaning. Maybe I can clean your ship. Make sure it's nice and tidy. I'll be your personal janitor!" The Doctor raised an eyebrow at this statement, shaking his head slightly.

"Bobby, you wouldn't have any chores," the Doctor responded, "You'd be a guest and I would never ask you to clean up after us. Besides, the Old Girl is extremely particular about how she likes things organized. I've gotten in trouble several times for reorganizing items or rooms to her disliking. She's extremely temperamental." The Doctor rubbed the back of his head in memory. Bobby watched him curiously, letting the information absorb into his mind. Those two were strange. Donna snorted with mirth, remembering that moment.

"She mentally slapped him and angrily hummed, darkening the lights. After, she dumped Spaceman on some deserted planet and dematerialized," Donna exclaimed. Covering her mouth with laughter, "I've never seen anything like it before. It was hilarious!"

"Oi, She was having an off day," the Doctor retorted, "She apologized afterwords for her harsh treatment. I'm surprised she kept you aboard though. Normally when she flies off in a huff she kicks everyone out."

"She just likes me better than you," Donna cheekily stated. Her eyes squinted teasingly. The Doctor scoffed playfully and rolled his eyes.

"Probably does," He agreed, "We've traveled together for at least seven hundred years. She's my oldest friend and longest companion. I guess we do get on each others nerves a lot. That's what happens when we're together 24/7." Donna laughed. Bobby's eyes darted between his two friends. Were they speaking in code. They talked about the spaceship as if it were alive. Bobby's eyebrows shot to his hairline.

"Doctor, is your ship alive?" Bobby asked curiously. He moved his checker piece up another space, watching the Doctor's facial expressions. He was clutching his stomach as he laughed, slightly wincing in pain.

"Yep, She's alive," the Doctor responded, before adding. "And the biggest brat too."

"Oi, like you have stones to throw, Martian boy," Donna retorted, grinning. The Doctor cheekily smiled back, winking playfully.

Bobby shook his head, giggling at his friends antics. They were so weird sometimes. He slid the board back over to the Doctor. The Doctor moved one of his pieces, before turning his attention back to the contraption he was building, a smile still playing on his lips. Bobby moved another one of his pieces. "King me," he shouted. The Doctor handed him a checker piece and Bobby stuck it on top.

"Mmm..this is taking forever," the Doctor muttered, using the regular screwdriver again. "If I had my sonic one it would be done." The Doctor picked up another piece, yawning.

Donna raised a brow at the yawn. She was worried about him and could tell he needed rest. When he first arrived, he had fallen onto his bunk with a painful groan. He had healed up since Bobby arrived, but the small winces and quick grunts did not escape Donna's watchful eyes. He had told her about the sensory test and how the night vision one took an awful turn with the werewolves. She was horrified to learn that he was punished for being injured and had lost his rights to food, water, and rest. Major Johnson also forced him, while injured, to train for four days straight. The scientist also added in a few scientific test as well. Mostly poking, prodding, and taking tissue samples. But it left the Doctor exhausted.

The Doctor had said that many of the training sessions were using weapons now. He was learning how to kill someone neatly and efficiently, which made him sick to his stomach. The Major had forced him to practice knife throwing, which he said he had hit the targets perfectly each time. He had gone to a circus once and the knife thrower there had taught him a trick using his wrist. Fencing was another one that he was forced to learn. The wielding of a sword and how to strike an opponent down, which he claimed to be well versed in as well. The four day training session must have been rough on the Doctor because when he arrived back, slash marks and bruises ran down his arms and legs and covered his face. Either he was being flippant and was punished for it or he wasn't as fast as he claimed to be. She thought the earlier idea was the most likely cause to his accumulated injuries. She watched as he switched between playing with Bobby and building his contraption. She had told him to rest, but he quickly refused saying that it was more important to get out of here.

_Swoosh chunk._ The large metal doors opened quickly. The Doctor's head popped up and he quickly grabbed his device, hiding it back in the hole before leaning against his bed casually. Bobby quickly scrambled up and started picking up the checker pieces and putting them away. Donna stepped over to the front of her cell. Two muscular stone faced guards approached the cells.

"Good day," Bobby happily chirped with a smile, "I was just finishing cleaning." Bobby placed the checkerboard and pieces underneath the janitor cart, quickly pulling out a mop and cleaning the floors, he watched the guards approach Donna's cell and the Doctor growled darkly.

"Leave her alone," the Doctor ordered, banging a fist against the wall. "She's human and you only deal with aliens. What do you want with her?" The guards ignored the Doctor, summoning Donna out. Donna stuck her chin up high and marched out of her cell.

"Where are you taking me?" she sharply questioned, crossing her arms and giving the guards a pointed glare. The tallest guard glance at her, before pushing her forward. "Colonel Graham wants to speak to you."

Donna glared, before stomping forward. "Good. I want to speak to him too."

The Doctor sighed. This was going to get ugly. Knowing Donna, she would probably insult the man and shout a bit to make her point clear. "Donna!" he shouted.

Donna turned her head, her blue eyes dancing with rage and determination. "What?" she bit back icily. Her face was set in a scowl and her eyebrows knitted crossly. This was not good.

The Doctor sighed, massaging his temple. "Just...Just be careful alright? Don't say anything that will provoke him." Donna's glare softened.

"I'm a big girl Doctor. I can take care of myself." The guard shoved her forward and she stumbled slightly. She turned sharply, placing her hands on her hips indignantly. "OI! Watch where you put your hands you brute." She stomped her foot and marched out the cell block doors. The Doctor sighed and glanced over at Bobby, who shrugged. He slowly sat down on his bunk and buried his face into his hands. "Be careful Donna. Please?" He whispered, slumping slightly.

* * *

**Hope you enjoyed this chapter. Next one will be the 'conversation' between Donna and Colonel Graham which should be interesting. :) following that is the drug test. If people want any specific drug to be tested on the Doctor, please let me know and I'll decide which one would be the best for that chapter. Thank you again for all your encouraging reviews and I'll hopefully update tomorrow, if not the following day. :)**


	21. Chapter 20

**Please review! I love reviews!**

Chapter 20

Donna was in a office. She sat in an uncomfortable chair, with black leather seating and a wooden frame. The desk was large and wooden and on the other side were drawers and a large black chair. The walls were covered top to bottom with military achievements, organized meticulously on the creme colored walls. She was pretty sure there was probably a second office with the same achievements in it. The office had more character and color than the rest of the organization. It made her hate the Colonel even more than before. The two guards who brought her in stood next to the door they entered through. Their arms crossed in front, eyes staring straight ahead.

Donna noticed a picture on the Colonel's desk. In the picture was the Colonel, a beautiful woman with long blond hair, and two children a little boy and girl. All grinning happily at the camera. Donna scoffed in anger. How can a man this cruel have a family. Torture aliens by day go home to a wife and kids by night. They probably didn't even know what he was doing. If they knew would they be horrified by his job or treat him like a hero who slayed the evil monsters that lurked in the dark? Donna's chest clutched with anger. She wanted to slap someone but she did hear the Doctor's warning. Maybe she wouldn't hurt the Colonel...much.

A second door was situated at the far end of his office on the right. She watched the knob turn and a man dressed in military fatigues stepped out. The screams of some poor alien being tortured came from the room behind the door. The door slammed shut. Donna's face paled with disgust. Sunglasses hid the Colonel's true eye color and his gray hair was cropped short. His muscular arms were crossed behind his back and a scowl was on his face. How could this be the man from the pictures? He swiftly and intimidatingly marched over to Donna. Donna sat up straight, matching the Colonel's scowl adding a death glare of her own. His hands were hidden in black leather seemed to be poking out at the tips. He sat down in the tall leather chair, folding his hands on top of the desk. Donna did the same. He pulled out a gray folder and flipped through. "You're a long way from home Ms. Noble," He stated coldly.

Donna bristled with anger and she felt her temper flare once more. "If this is your way of intimidating me you're doing a bloody awful job," she retorted, "I'd suggest some lessons, but that would only encourage your psychopathic tendencies." The Colonel didn't respond, instead flipping through the pages of the file, before turning his blackened gaze back at Donna. Her features reflecting off his sunglasses.

"Says here your records went missing after the Earth was moved,"the Colonel stated, "I had sent a few of my men to find somethings out about you, but they came back with little to no information. No school records or job information. They couldn't even find medical records or birth certificates. Its like you never existed. My guess is you ran off with that alien and decided to live under the radar of your old life. Now my question is what happened?"

"I don't know what you're talking about," Donna replied acidly. She straightened in her seat, scowling at the Colonel.

Colonel Graham coldly smiled. "Of course you don't Ms. Noble because it hasn't happened to you yet. You're too young in your timeline. Long ways from your home and year aren't you." Donna glared at the Colonel, keeping her mouth shut. The Colonel got up and circled the desk, stepping closer to Donna. "How long have you been traveling with the Doctor?"

Donna quickly shot her eyes over at the Colonel. "Why do you want to know?" The Colonel's gaze never left Donna's and his gloved hand ran across her shoulders. He didn't answer and Donna's face heated up with rage and she quickly slapped his hand away. "Don't touch me," she hissed, "About a year. Why?"

The Colonel nodded his head, stepping away, his hands crossed behind his back. He walked back behind the desk. "How much do you know about the Time Lord?" Donna glared.

"Who do you think I am his psychiatrist," She retorted sarcastically, "I don't know anything and tend not to like prying in other people's business. Unlike some people." She directed the last part at the Colonel, who stared at her impassively. "Even if I knew something I wouldn't tell the likes of you," she hissed. "I would never betray my best friend's trust." The Colonel sneered at Donna and she gave the same look right back, leaning closer.

"So you do know something," he concluded. He walked closer, getting into Donna's face. His hot breath brushing her nose. "You know I can break every bone in your body to get whatever information I want out of you."

Donna leaned closer, her blue eyes squinted with defiance. "and I'd take that pain and never give you any of the information you want. I would never betray my friend. I'd rather die," Donna replied back, her voice even. A small smirk graced her lips, "Your breath stinks. You might want to start using mouthwash." Donna knew it was a low hit, but she wasn't going to let this guy intimidate her. She was pretty sure he wanted information about the Doctor's weaknesses and other things that could crush him, mentally,emotionally, and physically. He wanted to destroy the Doctor. Make him obedient. A good little soldier. Well, she wasn't going to help with that. If they wanted information, they would have to find it themselves. Which would, basically, be impossible if the Doctor didn't want them knowing something. So, what does Colonel Jackass do. He interrogates her, thinking he could scare her into becoming a traitor. Well, Donna Noble was made out of tougher material than that sunshine. She stood her grounds, as the Colonel snarled. There was something strange about him. He didn't seem like a normal human being. Almost alien. Maybe he was an alien. But why would an alien want to be in charge of a place like the Underground?

The Colonel grunted and, like a hawk on its prey, circled Donna. His eyes never retreating from Donna's. "It must be quite shocking visiting other planets," he stated conversationally, "Seeing all those monsters. The aliens who willingly take lives and torture the innocent." Donna shot him a smirk.

"Sounds like a few humans I've met recently," Donna retorted. The Colonel growled at the quip.

"Do you hate your species Ms. Noble," the Colonel asked, "Has that _alien_ corrupted you already with fantasies of escape and adventure? Because you know that creature doesn't really care about you. They don't have the feelings humans have. Oh, they try but the monster underneath always awakens and it comes. Murdering your whole family and leaving you broken and lost." Donna didn't respond to his rant, instead listening and picking out information that seemed personal. "They need to be controlled. Have a human take charge and tell them what to do. They don't have the higher thinking to make moral decisions." Donna scoffed at the last part. If the Colonel ever met the Doctor, he would be sticking those words back down his throat. But the man was to high on his horse and was suffocating on the fumes of hatred. "That's why the Underground was developed. All those non-human creatures out there causing problems, all they need is a place where us humans can take charge and change them to benefit Earth. They're tools and we give them a duty to serve a superior race. But there are to many of them and not all are beneficial to our goals." Donna glared, crossing her arms.

"Are you going to play the James Bond villain at this point," Donna asked, sarcastically. "Spill the beans about your evil plan. Lets skip the whole evil speech and cut to the chase." Donna leaned closer. "I don't agree with any of that nonsense you spouted from that mouth of yours. I have traveled to different planets and met so many different alien species. What I have learned from this experience they are just like us. Trying to survive and take care of their families." Donna leaned closer to the Colonel, her steady glare never wavering. "Yes, you get the cruel tyrannical villain but that's the same with humans. The universe is a big place Colonel Graham, but its not big enough to fit people like you." The Colonel lips lifted in a hateful sneer. Donna's face reflected off the black glass.

"I guess you've chosen a side than," The Colonel growled. Donna slammed her hands on the table.

"I guess I have," she stated confidently, her glare steady and defiant.

"The side with the monsters,"The Colonel concluded, sneering. Donna lifted her chin.

"No, the side _against_ the monsters," she responded, directing a pointed glare at the Colonel, expressing who she thought the monster was. Colonel Graham snarled in frustration, slamming his fist on the table. The table shook.

"Since you're a traitor, you'll be treated like a traitor,"the Colonel stated coldly, "You'll be fed what the aliens are fed, you will wear what the aliens wear, and you will have no rights. The guards and scientists can do whatever they please with you. You will no longer be under my protection."

"I live in a cell, sunshine," Donna retorted, "I think I can handle whatever you dish out." Donna paused for a second, before a brave smile twisted her lips. "That reminds me, I have a few complaints about the way you treat the aliens. The food smells like puke and is extremely unhygienic. You may want to clean up those meals before the health inspector comes snooping about. Your kitchen might get shut down." The Colonel stiffened and every muscle in his face tightened with anger. Donna only smirked at the reaction, if he was expecting her to fall to her knees and plead for mercy,he wasn't getting it.

"You're no longer considered human from this point on," the Colonel stated, "Your words mean nothing to me and your complaints will not be heard. You will live in the same conditions like the rest of those freaks." The Colonel turned away from Donna, glancing at the guards. "Guards take _it _away and remove those _human _clothes. I want _it _dressed in the standard prisoners garment immediately. Also, alert the cook about the new food schedule. Tell him, he no longer has to make the chicken and potatoes." The Colonel glanced at Donna one last time. "Get _it _out of my sight."

The two burly guards marched forward, grabbing Donna's arms and lifting her from the seat, they dragged her and Donna kicked out. Aiming one of her kicks steadily into the guard on her lefts shin. He grunted in pain, releasing her. She landed a slap on the guard to her right. She stomped forward. "I can walk fine, thank you," She stated acidly. The Colonel watched the scene slightly amused, though the expression on his face was cold and indifferent. Donna whipped her head around, giving the Colonel a defiant glare. "I don't know what happened to your family and I am sorry for your lost. But hating and torturing people is wrong. We will stop you." The Colonel's mouth twitched in contempt.

"I don't think you're in a position to make threats," the Colonel responded. His arms placed behind his back, as he stood up straight.

"I think I'm in the perfect position," she retorted. The Colonel's teeth gritted with anger. He turned away, picking up the bottle of gin, and poured himself a cup. He took a sip and flitted his hand. "Take _it _away," He ordered. Donna was frog-marched out of the room, slightly stumbling from the sudden force.

* * *

Donna entered the cell-block. The loud clipped marches of the guards behind her. Her bare feet slapped the cold white floor. She wore what the Doctor wore. A baggy cream colored shirt with thin pants. The guards shoved her forward and she turned quickly, giving them the death-glare. She glanced forward and saw the Doctor watching her, Jake standing next to his cell. Donna nodded to Jake and he hesitantly waved, before picking up his cattle-prod and other gear. He quickly nodded his head respectfully at the two guards and winked at Donna, quickly leaving the cell-block. The large metal doors slamming behind him. The guards shoved her roughly into her cell, which initiated a threatening growl from the Doctor.

"Be careful with her,"he ordered. The guards ignored his request, instead swiftly turning on their heals and marching away. He turned his gaze back to Donna, looking her over thoroughly. She didn't seem beaten or bruised. "Donna are you alright?" Concern laced his voice. Donna turned to face him and smiled brightly.

"Fine," she chirped, "Just told the Colonel whats what and he decided that I was a traitor to the human race. Apparently, I am no better than the alien's down here. So, guess what sunshine...I'm your equal now." Donna winked and the Doctor's frown deepened. He ran his fingers through his dark brown hair, glancing concernedly at Donna.

"Did he hurt you?" The Doctor asked. He felt his blood boil at the thought, causing his eye to twitch slightly.

"Nope," Donna responded, popping the p. "I think I may of damaged his ego slightly though. He was trying to recruit me into his hate group and I flat out refused. I think he was, also, fishing for some information about you. Most likely weaknesses. I think he assumed because I was a woman I would gladly gossip about my friends. Jerk." She glared slightly, before glancing over at the Doctor's worried brown orbs. She rolled her eyes slightly. "Oi, Spaceman. Don't worry about it. I can take care of myself. Now, tell me what you were talking to Jake about. I'm curious." She ordered slightly, giving a playful glare. She wanted to take the Doctor's mind off the current situation. He didn't need anymore problems to stress out about.

The Doctor let out a breath, massaging the back of his neck. "Yes, quite right," he started, "Oh nothing much, just basically the same thing you and Jake talked about. Also, told him a few of my adventures to lighten the mood. The boy was jumpy, nothing like his alternate self. But, I guess when you work in a place like this, monsters are at every corner." The Doctor forced a smile on his face, but his eyes expressed his true feelings about the situation.

Donna stared at him dumbfounded. Sometimes the Doctor just didn't make any sense. "Alternate self?"

The Doctor glanced over. "Hmm...yes. I haven't told you that. I've met Jake Simmonds before. Well, his alternate self. A lot different actually, that Jake's hair was more spiky. Me, Rose, and Mickey crashed in a alternate universe. Fought cyberman and saved the day." The Doctor quickly glanced over at Donna, to check if she was following. "This is this universe's Jake Simmonds. He's a little older than the alternate Jake but that's probably because we're in 2015. Weird, huh?"

Donna stared at him, her mouth slightly gaping. "You are bonkers," she stated exasperatedly.

The Doctor nodded his head. "Well," he replied, clicking his teeth together. He shrugged.

Donna shook her head. "I give up."

The Doctor smirked, before clearing his throat. "He has somewhat of the heroic side that alternate Jake has. He agreed to help us with any escape plans, by not telling anyone and leading them the opposite way when our escape date comes. But he doesn't want to risk his life and that's completely understandable. He's a good man, just has a terrible job. I told him I'd help him get out. I guess the only way you can escape the employment of the Underground is by either memory deletion or death." Donna nodded her head. A frown steadily growing on her face. This place was horrible and needed to be shut-down. Donna's lips curled in disgust. She glanced over at the Doctor.

"Doctor, I think Colonel Graham is an alien," Donna blurted out. That whole confrontation was strange, with the Colonel wearing sunglasses and black gloves and his lips constantly curled in a snarl. It just sent shivers down her spine.

"Nah," the Doctor responded. His brown eyes stared at her curiously. "Why do you say that?"

"Oh, nothing,"Donna replied hesitantly, "Just that sometimes he didn't seem human."

The Doctor nodded his head. "I've already met the Colonel on my first day. He seemed perfectly human to me. A bit of a jerk though. I didn't notice any holograms that covered him or a body suit. So, I don't think he's an alien." Donna quirked an eyebrow, leaning against her bunk she had stepped over too.

"Maybe it recently happened," Donna stated, "like some weird alien parasite crawled into his ear and took over his brain. Or one of the prisoners escaped and possessed his body. I don't know. He just seemed off."

The Doctor shrugged, "Could be, but I doubt it." The Doctor strode over to his bunk and flopped down. His eyes gazing at the ceiling. "I'll keep an eye out."

Donna nodded her head, laying down on her own hard bunk. "Good. Get some rest, Doctor. I don't know when the guards will come back to collect you."

The Doctor nodded his head drowsily. His eyes slipping closed. "Night, Donna," he stated, yawning. The lights had switched off a few minutes ago.

"Night, Doctor," Donna replied. She curled up onto her bunk and slowly drifted to sleep.

* * *

**Thank you for all your reviews. :) I loved them all and they made me really happy. Some of your ideas for the drug test were incredible and if I don't use them now, I may use them in future chapters. Thank you again for all your support and I hope you enjoyed this chapter. Thank you again and keep reviewing. :)**


	22. Chapter 21

**Hey, thank you everyone for reviewing. :) Sorry if commas have not been in the right place. That is one of my main difficulties, but I think I'm getting better. My main problem is trying to decide where a comma is needed. So, yeah thank you to all who pointed out comma mistakes, its a learning process for me and critiques are helpful to my developing writing skills. :) I am glad you're all enjoying this story and I know many will have questions, but everything will be explained, either in this story or other stories and one-shots I create. :) Thank you again and I hope you all will continue reviewing. :)**

Chapter 21

The Doctor laid on a hard metal table. His arms, legs, and torso strapped down. His head was unable to move. He was in a lab of some sort that smelled strongly of chemicals. The Doctor took a long sniff, quickly categorizing the smells. He sighed. Each chemical smelled like some type of drug. He was definitely in a drug testing lab. The Doctor squirmed a bit, pulling at the cuffs. The cuffs didn't budge and a defeated sigh passed by his lips. The metal was cold on his bare back. He shivered as the cold metal caressed his skin. His brown eyes darted around the room, picking up details, and storing them into his memory. The lab looked like any other lab, with counters along the wall and beakers sizzling over an open burner. The Doctor swallowed thickly. He closed his eyes and sighed. He really didn't want to deal with this today. He yanked a little harder on the leather cuffs, but even his superhuman strength couldn't break the bonds.

The doors flew open and Dr. Black marched in. A young assistant following behind. Her high-heeled shoes clipped loudly on the polished white floors. The Doctor's brown eyes met cold blue. Dr. Black's face was set with an indifferent expression as she peered down at him. Her short brown hair tickled the Doctor's nose. A cold clinical hand ran along the Doctor's bare chest, pinching and poking. She never once spoke to him or acknowledged him as a person. The Doctor shivered slightly under her touch, turning his gaze towards the young assistant standing behind her. The assistant held a clipboard in his right hand and a pen in the other. The Doctor hissed as she pressed down on his ribcage. It was still sore from the last test and the intense training that followed. She raised an eyebrow slightly at his discomfort before pressing down harder. The Doctor screwed his eyes shut, groaning. The young assistant quickly jotted down the reaction. Dr. Black's hand slid down lower, her fingers playing along the scarred skin, tickling under the ribcage. The Doctor's face flushed with embarrassment.

"Can you not feel me up," he asked. His voice squeaking slightly as her chilly hands ran along his stomach. Her clinical gaze never once leaving her work. The Doctor wriggled under the scrutiny, desperately trying to escape the lime-light. He squeaked in surprise as sharp nails dug into his bare chest. A threatening glare was directed at him.

"Stop moving," she icily ordered. She retracted her nails from his skin, leaving five neat nail shaped holes. Reddish orange blood dripped down his chest. "You're messing up my evaluation." The Doctor nodded his head, closing his eyes as the poking and prodding continued. This was humiliating.

"It seems Subject 13 is a fast healer," Dr. Black stated, turning to her assistant. "Most of these injuries it had received have scarred over. The scars are also disappearing rapidly fast. Most aliens who gain these type of injuries would not pull through or heal quite as quickly. This new discovery has opened up questions about its healing factor. How fast can it heal and how exactly does the regeneration energy work? It has been rumored that if subject 13 is killed it would grow a new body. This is something we would need to study in the future. But for now I want to see how different drugs affect a Time Lord's physiology." Dr. Black stepped away from the metallic table.

The Doctor warily watched her walk over to one of the counter and pull out a syringe and needle. She pulled out a capped bottle from one of the cabinets. She placed the needle onto the syringe before checking the plunger. She stuck the needle into the bottle slowly filling it up. She squirted the clear liquid out, making sure it worked. She strode back over to the Doctor. Needle and bottle in hand. She glanced over at her assistant. "Write this down," She ordered. The assistant immediately begun writing down everything she said. "Today we'll be testing the alien drug, Rapzy, on subject 13. We have tested it on several other subjects and found it had a similar affect and side affects to heroin. When previous subjects were given a high dosage of Rapzy they became very slow and relaxed. The drug made them sleepy and relatively happy. The withdrawal side affects, after the dosage wore off, were quite violent. The subjects were restless and extremely nauseous. Vomiting and diarrhea was two of the many symptoms, including muscle and bone pain and cold flashes. The subjects temperature had increased to dangerous levels and we were forced to dump them into an ice bath." Dr. Black glanced over at her assistant. He rapidly jotted down everything she said, before nodding his head in the 'ok' gesture to continue.

"Rapzy,as we found, has proven to be highly addictive. After only a couple of doses the subjects struggled and begged for more,as their bodies slowly shut down from withdrawal. The symptoms lasted three to four days. After those few days the subjects still wanted more and every time they saw the bottle, they reacted strongly. Fighting the guards and scientists. It was an immediate addiction and was difficult to remove the craving."

Dr. Black glanced down at the Doctor. His face had paled considerably. He knew what Rapzy was and it was illegal on most planets. It was highly addictive and if somebody overdosed on it, it could cause permanent brain damage or death. The Shadow Proclamation had their hands full dealing with Rapzy Trafficking. The drug was considered extremely valuable and most aliens were willing to lose everything for that drug. This caused drug traffickers to favor it above most other drugs. The Judoon had set up security at most spaceports because people would hide it in their luggage or try to sneak it onto spacecrafts. The withdrawals were terrible and many times people continued to take Rapzy to avoid its inevitable symptoms. The Doctor wondered where Dr. Black had attained Rapzy. The most likely conclusion, from either an addict or Rapzy trafficker that the Underground had captured and plundered the ship.

"Today, we will be testing how many doses it takes to affect subject 13. Our goal is to cause an addiction. The average dose is normally one to two servings, but subject 13 has shown higher tolerance to many other treatments, including electricity and deadly wounds. I will be giving the first dose now and after five minutes of watching for side affects, I shall give the next dose and so on. I will record its reactions to the drug as I add more of the drug into its bloodstream." Dr. Black glanced over at her assistant as he wrote down the last few notes.

The Doctor frowned. This was not good. He didn't say anything though, knowing that his words would fall on deaf ears. His muscles tightened in anticipation as Dr. Black slid the needle into his skin, releasing the liquidized Rapzy. Dr. Black yanked the needle out viciously. Her face showing no emotion. Her eyes were bitterly cold, except for the slight glimmer of fascination. She turned to her assistant. "I think after this we should test out a few other drugs. Human drugs. What would you suggest?"

The assistant glanced between the Doctor and Dr. Black, his hand stroking his goatee in contemplation. He lifted the clipboard and wrote down a couple of possible experiments they could play around with. " I was thinking Nitrous oxide. That could be interesting seeing how it effects different alien species. I also was thinking that emetics or aspirin could be interesting to test out too. Maybe a few viruses, like ebola, in the future as well. Its good to discover what could kill the alien efficiently, so we can dispose of it when we're through." Dr. Black nodded her head, tapping her lips.

"Yes, but its also good to find out its weaknesses so we don't kill it early," Dr. Black replied, "I think the Colonel is planning to keep this one around for a long time. I also plan on using it to test out new pharmaceutical drugs or cleaning chemicals to make sure they're safe for the general public and won't kill children or pets if they take a bite."The Doctor paled at what his possible future held. The drug hadn't taken effect yet and his body's immune system was working hard to rid the dangerous toxin. But he knew it would fail at some point when his body became to heavy with the toxins.

"Besides I think the plan is when its usefulness grows thin, its last test will be the dissection room. Dismembering its body and finding out if any of its parts could benefit the general society. I wouldn't want toxins to get in the way at that point,"Dr. Black explained. She slid the needle into the Doctor's arm, adding more of the dangerous drug. The Doctor felt a slight buzz, as the drug slowly begun to take effect. But it wasn't strong enough to fully take over. The Doctor's eyes fuzzed out slightly and he felt his mouth grow dry.

Dr. Black stuck her finger into the Doctor's mouth, feeling around, before lifting his eyelids. His eyes were slightly clouded. In a clinical voice, she noted. "Subject 13 has been given a second dose and changes have been immediate in his biology. Its mouth has slowed down the production of saliva and his eyes are unfocused. But this reaction, I believe, is caused by its body reacting to the unknown substance that entered the bloodstream. I am sure a few more doses will give the appropriate high that Rapzy causes." The Doctor dazedly watched Dr. Black prep another needle. He groaned. He was still coherent and understood what the scientist and her assistant were talking about.

"But the files say its the last of its kind," the assistant stated, "Once its gone we won't have its unique abilities and other factors." Dr. Black glanced over, before giving the Doctor another shot of the toxic poison. The Doctor felt his eyelids grow heavy. He suddenly felt extremely sleepy and relaxed. His legs and arms felt heavy as the drug took over. Dr. Black filled a forth needle, before prodding the Doctor's muscles. The assistant took careful notes and data on the new physical changes.

"Yes, that is quite true. It would be a shame to lose its abilities," Dr. Black agreed, "And I have discussed it with Dr. Carter. He came up with this brilliant plan that he's considering proposing to Colonel Graham. He has been curious about how aliens reproduce and wanted to open up a breeding pen." The assistant's eyes shot up to his hairline.

"A breeding pen? But I thought the Underground's whole goal was to limit or terminate the whole non-human population. Wouldn't that just increase it?" Dr. Black nodded her head in understanding, before inserting the fourth needle into the Doctor's arm. The Doctor could barely listen to the chatter. His mind was on a strange buzz and his mental functions had slowed down immensely. He couldn't think straight and he let out a strangled giggle. His mouth gaped open and drool slid down his chin as his saliva ducts begun working rapidly once more. He lazily tried to focus on Dr. Black, but every motor function was shutting down.

"Yes, but we have plenty of technology to control the breeding. We don't have to use natural birth only. That would only be a onetime experiment. Think about it. We have a cloning machine that we salvaged from a crashed ship. With that alone we helped Earth develop cloning quicker than it would of alone. Also, we have a genetic splicer. We can take a couple of tissue samples and voila instant baby. If we were developing baby aliens inside the Underground, we could better control them. The one problem we have with the aliens now is that they remember and are familiar with freedom. But if we had a baby alien born and raised here, it would not understand the concept of freedom. It would be completely at our mercy and control." A smile crawled across Dr. Black's face and she stabbed the fifth needle into the Doctor's arm.

Black spots appeared in the Doctor's eyesight and he crinkled his brows in confusion. "Wha?" he slurred. Bright colors flashed before his eyes and he giggled happily. He felt light-headed. His respiratory system had slowed down considerably and his hearts were now a dull thump. At this point he felt like he was floating amongst clouds, before a sudden heaviness took over again. More lights flashed and they took different shapes. He crinkled his nose, moaning. "Go away puppy," he slurred, before speaking rapidly in Gallifreyan. His hearts beat increased as panic took over. He screamed and struggled in his bonds.

Dr. Black watched the reaction and turned to her assistant. "Write down hallucinations. That's a new one." The assistant quickly wrote down hallucinations. The Doctor's hearts beats slowed down and his breathing became less sporadic. He calmed as he entered a new level to the drug. His body relaxing and he sighed as his eyes heavily drooped. Dr. Black turned back to her assistant.

"So, yeah. We have considered attempting the development of a second Time Lord. It will be difficult since its a rare alien specie. But me and Dr. Carter are developing the formula and plans to make the creation a success. In this case when the older one outgrows its usefulness we'll have a second one to carry on its legacy."

Dr. Black slipped a sixth needle into the Doctor's arm. The Doctor shivered as the extra toxins spread through his body. He cried out in surprise as another hallucination took form. "I think that will do," Dr. Black concluded, throwing the syringe and needle away and putting the Rapzy back into the cabinet. "Overall, I find it a good idea to keep obedient aliens around. The Underground will still have enemies that need to be overthrown."

The assistant nodded his head in agreement, quickly taking notes on the Doctor's reaction to the drug. The Doctor seemed to go back and forth between extremely drowsy to extremely awake and active. Which proved that Rapzy could either be a stimulant, a depressant, or both. The Doctor had stopped wiggling instead staring glassily at the ceiling. His mouth hung open, dry again. He slapped his tongue against the roof of his mouth, trying to obtain moisture. His face had paled considerably and his emotions switched rapidly between giggling hysterically or crying uncontrollably. Every muscle in his body felt like lead. Tears sprung from his eyes and slid down his cheeks, before abruptly stopping. He felt terrible. He couldn't keep track of time and he felt himself nodding off, before jerking awake. Dr. Black's and the assistant's conversation became a dull hum in the back of his mind as he slowly fell into a drug induced slumber.

"Subject 13 reacted much differently, than I expected, to the drug," Dr. Black concluded, "Most of the other aliens had reacted sleepily and relaxed as the drug took over. But Subject 13's drug induced state switched between heavy sleepiness to hallucinations and paranoia. It has opened more questions to subject 13's unique biology when compared to other aliens and humans physiology."

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**Thank you all for reviewing. I hope you enjoyed this chapter. The next chapter will be the drug withdrawal. The other drugs that I mentioned may or may not be used in future chapters. It was just showing that the scientists believe the Doctor will be sticking around for a while. Plus, I wanted to mention some of your awesome ideas. :) I hope you review some more and I will hopefully get the next chapter out by tomorrow, if not the following day. :)**


	23. Chapter 22

**Thank you for all your wonderful reviews for the last chapter. I was planning on updating yesterday but I had a busy day. :) Glad you're enjoying the story. Please review. I love reviews!**

Chapter 22

"NAHHHH!" The Doctor screamed, wriggling on the medical bed that he laid on. Sweat ran down his face and his teeth gritted in agony. His eyes were screwed shut and he panted heavily. The bed covers were strewn and tangled as he kicked, twisted, and writhed in pain. He wanted it to stop. Bile soured his throat as it flowed up his esophagus, bubbling out of his mouth, and sliding down his chin. His hair was plastered to his forehead, soaked in sweat. Another blood-curdling scream exited his mouth and his fingers clutched the wet sheets. Tears sprung from his eyes, rolling in fat drops down his cheeks. He hissed and cried out as another wave of nausea and agony hit him. Dark circles had formed under his eyes and his skin was a sickly pale. His freckles standing out darkly against the pale background of his skin. The Doctor whimpered. His skin slick with sweat. His mouth gaped and his body twisting in distress. He turned over. _Blah. _Vomit splattered the floor in large greenish-brown clumps. The putrid smell of barf reached his nose and he moaned. His body switching between extremely cold to extremely hot. He coughed up blood, shivering from the force of the cough. His skin rose in goosebumps.

He struggled to open his eyes as he heard the familiar clip of heels and the rough march of two guards. He couldn't focus, eyes shutting heavily once more. A new wave of nausea hit. His skin prickled with sweat. He gritted his teeth in pain. His stomach twisting in discomfort. His hearts thumped quickly, straining from the panic his body endured.

A cool hand touched his burning forehead. The fingers brushed his hair back and he sighed in relief from the cold touch. He heard a beeping next to his left ear, but the sound was far off. His head moved side to side, trying to locate the sound. He moaned as the hand was removed from his head. His head pounding in pain. His eyelid was lifted and a bright light shone into his brown orbs. He squealed in surprise as the light burnt his eyes. He struggled slightly, but two strong arms held him down. The light was turned off and his eyes snapped shut quickly. The cool hands roamed up and down his body. Each touch felt wonderful against his burning skin. The hand came back up to his face, tickling his ears, and lifting his top lip. The Doctor breathed heavily. Each breath painful and struggled. The cold hand left his hot body again. He heard snippets of a conversation taking place.

"It has a high fever..." a female voice stated. The voice sounded familiar. "The withdrawal affected subject 13 a lot worse than I expected..." the voice begun to die down, the last thing he heard was "...Ice bath." The Doctor cracked an eye open, squinting painfully. He glassily spotted a woman with short brown hair, before his eyes snapped shut.

"Gross," another voice said in disgust. The Doctor turned his head to the sound, "It threw-up." The Doctor squirmed as two strong arms lifted him up, holding him bridle style. His hand shot out, grabbing the guard's shirt. His fingers twisting into the fabric. He moaned as he was bumped around painfully.

"I'll call the Janitor," Another voice stated. The Doctor heard a slight ringing. His head bent backwards, hanging over the man's arm. Mouth gaping. The guard suddenly jerked and the Doctor's head flopped painfully. A new wave of nausea crashed. He groaned.

"Damn," the guard holding him cursed, "This thing's heavier than it looks." The second guard chuckled at the first Guard's struggle. The Doctor cringed from the loud piercing noise and squirmed a little. "Quit moving," the first hissed, shaking the Doctor a bit. The Doctor moaned as his head hit the muscular arm. His stomach twisted and he felt the rest of last night's dinner rise.

"I'll check on Dr. Black," the second guard stated. "See if she's ready for it." Heavy footsteps clomped on the floor as the guard exited the room. The Doctor tightened his grip on the shirt. He moaned loudly as another wave of pain hit.

"Oi, loosen up freak," the guard ordered cruelly, "You'll rip my shirt." The guard took a heavy step forward as he followed the second guard. The Doctor groaned from the sudden jerk and his head lolled back. Tears dripping down his cheeks. The Doctor pulled his head up slightly. His face turning a light green. _Blah. _Throw-up sprayed all over the guard. The greenish-brown clumps slowly rolled down the uniformed shirt. A look of pure horror and disgust graced the guard's barf-splattered face.

The Doctor slumped slightly in the guards arms. _Thump._ He hit the ground hard, shrieking in surprise as his head collided with the cold tiled floor. A swift kick was driven into his stomach and he cried out in distress. He curled in on himself, bile sliding between his lips. Rough calloused fingers twisted in his wet hair, violently yanking him up to his knees. The guard continued to pull him up and the Doctor screamed in agony from the rough, uncaring treatment. Every part of his body hurt. He was exhausted. The guard threw him across his shoulder, treating him like he was nothing more than a sack. The Doctor's arms hung down. His breaths coming out heavy. The guard marched down the hall and towards the ice bath, grumbling in anger.

* * *

The Doctor let out a startled scream as he was dropped into icy cold water. The water bit at his burning skin and he struggled in shock from the sudden change in temperature. He kicked out his feet. His foot colliding with someone's face. Crying out, he tried to climb out of the bath but two pairs of strong arms held him down. He writhed and squealed, begging to be released. But his pleas fell on deaf ears. Icy cold water was dumped over his head. He shivered as the ice water slid down his face. Coughing, he opened his eyes to the brightly lit room. His eyes burning in pain from the sudden brightness. He leaned his head against the bathtub rim, whimpering as another wave of nausea hit. He swallowed the bile that crawled up his throat.

Dr. Black's face came into view. Her blue eyes scrutinizing the Doctor. She stroke his wet hair back, placing a cool hand on his forehead. The Doctor's eyes lazily looked up.

"Its temperature is dropping," She stated. She stood up, marching away. The Doctor screwed his eyes shut. His lower gut twisted in agony. "Pull it out." The guards roughly yanked him out of the tub. He collapsed, curling up into a fetal position on the floor. Sobs wracked his body and his arm circled around his stomach.

He was lifted up into someone's arms and marched back to the med bay. The smell of sweat and sickness invaded his nostrils. He was dumped onto the bed he started in. The bed was saturated in sweat and bile and the covers were tangled in a heap at the end of the bed. He was no longer dirty with sweat, but extremely wet and cold from the icy water. He curled up and cried. He felt awful and couldn't do anything about it. He knew he should of fought back when they were injecting him with the drug, but no one would of listened to his reasoning anyways. So, he stayed quiet throughout the whole test. The Doctor's mouth gaped and he let out a pitiful sob. That one sob showed all the misery and frustration he felt. His fever slowly crawled back. He was burning once more.

* * *

"Doctor?" A familiar voice questioned. The Doctor swerved his head searching for the voice, his eyes closed shut. Somebody approached him. He curled up, expecting more pain. A pitiful whimper released from his lips. "Doctor,"the voice said again, approaching closer, "It's me, Bobby. Don't be afraid."

The Doctor's ears perked at the familiar name. He peaked a cautious brown eye out. His eyesight was still blurry but he could tell it was Bobby's outline. "B-Bobby," he stuttered, shivering from the sudden chills that wracked his body. Bobby smiled, kneeling down next to the Doctor's bed.

"Yes, its me," he said softly, "You don't look so good." Bobby's hand gently touched the Doctor's forehead, before drawing back. "You're warm." The Doctor closed his eyes, moaning. Bile once again crept up his throat. The Doctor's muscles and bones ached. Every time he moved his bones cracked and moaned in protest. But his body kept on spasming so each time he moved agony would rip through his nerves. He cried out, fingers twitching uncontrollably. A soft hand rubbed circles against his back. The bed dipped as Bobby climbed on top. Bobby sat next to the Doctor, humming softly.

"There there Doctor,"he cooed gently. The rhythmatic circles loosened his muscles. The Doctor sighed in relief as his body seemed to slowly relax. "I'll take care of you. My uncle was this sick once and I had to take care of him. I know what to do." Bobby lifted his hand and hopped off the bed. He made his way over to the janitor cart and pulled out a bucket. He softly tip-toed over to the Doctor, placing the bucket next to the bed-ridden Time Lord. Bobby sat back down next to the Doctor, shushing softly as he cried out and squirmed.

Bobby lifted the Doctor's head gently, placing it on the pillow. He stripped the bed of the sweat saturated covers and tossed them into the janitor cart. He pulled another blanket off one of the beds next to the Doctor's, draping it over his shivering shoulders. Bobby gently patted him on the head, before standing up once more. He walked over to the med bay sink and pulled out a cup, filling it with cool water. He quickly walked back to the Doctor, lifting his head. Bobby pushed the cup in front of him. "Drink up Doctor," Bobby calmly stated, "You don't want to die of thirst." The Doctor shook violently, his eyes popping open. He eyed the cup, before taking a tiny sip. The cold water trickled down his dry, sore throat. Bobby pulled the cup away before he could drink to much.

"Na uh Doctor," he quietly exclaimed, "You can't drink to much. You'll get even more sick. I've been sick before from drinking to much water. It doesn't feel good." The Doctor tiredly nodded his head, wincing in pain as the migraine he had developed wracked havoc on his already pain-filled mind. It was like a jackhammer decided to drill holes into his brain. The Doctor leaned back and closed his eyes. A thin frown was on his cracked lips. Tears prickled at his eyes.

A cold cloth was placed on his forehead. He cracked an eye open. Bobby sat next to him. He picked up the cloth and soaked it with chilled water, before placing it back on the Doctor. He stood up and walked over to the cart. He pulled out a mop and begun mopping up the throw-up.

"Well, isn't this an awful mess,"he exclaimed. He put the mop back into the soapy bucket. Sloshing it around, he slapped it back to the ground. The Doctor frowned and squirmed slightly under the light blanket.

"I-I'm s-sorry," he stuttered, gritting his teeth. A dry clump formed in the back of his throat. Bobby raised an eyebrow. He pushed his glasses up his nose and softly smiled.

"Nothing to be sorry about Doctor," he comforted. "Dr. Black should be the one taking care of you, instead of leaving you here alone. She's not a very good doctor." The Doctor bitterly chuckled, before moaning as his stomach reacted poorly to the movement.

The Doctor's throat soured as bile rose. His face turning a light green. The mop thumped to the ground and quick footsteps approached him. The bucket, next to him, clanged as it was lifted up. Bobby sat behind him and rubbed comforting circles against his back. He lifted the bucket to the Doctor's face. _Blah._ He couldn't hold it in any longer and the last bit of food from his stomach spilled out into the bucket with a splat. Vomit kept coming up and the Doctor coughed in pain. Tears slid down his cheeks as more vomit came out. _Blah. Ahem ahem. _He coughed loudly, panting heavily. His hair was plastered to his forehead from water and sweat. Bobby gently pushed him down onto the bed. He took out a rag and wiped away the vomit that lathered his mouth.

"Feel better now," Bobby asked quietly. The Doctor nodded his head, groaning. He licked his dry lips and glanced up at Bobby.

"T-thank y-you," he said. His eyes drooping heavily, he curled up into a ball. Bobby brushed a hand through the Doctor's wet hair, smiling softly.

"What are friends for," he responded. He stood, picking up the bucket, and dumped it out in the sink. He scrubbed the bucket clean before placing it next to the bed. He picked up the cup of water and slowly tipped it into the Doctor's mouth. The Doctor lapped it up greedily. Bobby pulled the cup away and placed it back on the bedside table before gently pulling the covers up to the Doctor's chin.

"I w-want m-more," the Doctor begged, slightly rolling over. He kicked off the blanket, groaning. He reached out a hand, clutching the blanket. His fingers twisting into the threads. "m-more," he moaned, reaching his other hand out towards Bobby.

Bobby lifted a quizzical brow at the writhing alien. The Doctor struggled in the bedding trying to escape. "More water," Bobby questioned, holding out the cup. The Doctor shook his head, coughing violently. His whole body jolted from the cough.

"More rapzy," he groaned. "I w-want the p-pain to go a-away." he shrieked as every muscle in his body burned in agony from his movements. He held out a hand, opening and closing it. "P-please." Bobby pushed down his hand, holding it tightly.

"What is rapzy Doctor," he asked. Worry evident in his eyes. He mopped away the sweat from the Doctor's face.

"D-drug," the Doctor responded, licking his lips. Bobby frowned and shook his head. He comfortingly rubbed circles on the Doctor's arm.

"No Doctor,"he said firmly, "I'm not giving you a drug. Just relax." He pushed the Doctor's hair back, playing with the strands. The Doctor gripped Bobby's arm, eyes burning with desperation. Bobby glanced at him startled from the sudden force. The Doctor gritted his teeth.

"P-please,"he begged, "I-it w-will m-make t-the p-pain g-go a-away." Bobby shook his head in determination, pushing the Doctor back against the pillow. The Doctor's eyes were glazed and clouded. His pupils dilated.

"No Doctor. You're addicted aren't you?" Bobby questioned, remembering something similar happening to his uncle. "You're going through withdrawal." He stroke the Doctor's hair back.

"I-I w-want i-it," The Doctor stated. Another violent spasm attacked his body. He shivered violently. Bobby shushed him gently.

"I know you do," Bobby said, "But once this is over you'll feel better. Just push through it." The Doctor let out a strangled cry,clutching Bobby's shirt.

"I-I'm s-so w-weak," the Doctor cried out. A new wave of pain and nausea assaulted his already abused body. "I-I'm n-nothing. I c-can't p-protect Donna o-or m-myself. I-I a-allowed t-these p-people t-to t-torture m-me b-because I-I'm t-too w-weak t-to s-stop t-them." The Doctor sobbed in frustration. "W-why?" he asked. His voice cracking from the strain. His eyes, a puffy red from the crying and drugs. Bobby hummed softly, soothingly rubbing his back.

"You're not weak Doctor," Bobby responded, "Don't you ever say that about yourself. You just hit a rough time that's all." Bobby took the wet cloth and wiped the tear away from the Doctor's face. "It can only get better." The Doctor's bottom lip wobbled as fresh tears sprung from his eyes. He put his arm over his face and sobbed. He didn't want to look at Bobby. The Doctor was afraid to see the disappointment and pity in his eyes. He was embarrassed and exhausted. The withdrawal brought out his deepest darkest emotions and self-hatred. This place was changing him and he knew it.

"Just keep fighting Doctor," Bobby stated, "Never give up." Bobby soothingly hummed. The Doctor peaked a swollen red eye out. He knew, at that moment, as long as he had people like Donna or Bobby around he would be alright. He would find a way to escape and shut down the Underground. Giving up was not an option. The Doctor closed his eyes. Bobby's humming lolled him into a restless slumber.

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**I hope you enjoyed this chapter. It was very emotional to write. The Doctor is a bit ooc, but anyone would be if they were going through a drug withdrawal. Please review and let me know what you think. :)**


	24. Chapter 23

**Thank you for all your wonderful reviews. They made me extremely happy. :D I hope you review more. So, here's the next chapter.**

Chapter 23

"Oof!" the Doctor roughly hit the hard floor as two guards threw him back into his cell. He groaned, his face smacking cruelly into the ground. Blood seeped from his nose and he slowly turned over onto his back. The force-field to his cell shot up and the soft buzzing of electrical current was heard. The reddish-orange blood trailed down the side of the Doctor's face. Brushing his hand across his nose, he tried to wipe away the bloody mess. He rolled to his knees still dizzy, nauseous, and craving the rapzy. The drug was powerful, considering it made a Time Lord addicted. He crawled over to the wall, leaning his forehead against the cool tiles. He was so tired. The withdrawal had affected his body and immune system greatly. After the withdrawal, he had caught a normal human flu that lasted a couple more days. He had lost track of time, during the days he was ill and didn't know whether he was gone for a week or weeks.

His hearts clenched with guilt at leaving Donna alone for that long. He knew it wasn't his fault but he mind as well blame himself. He was expose to protect Donna. That was his job. Make sure she got home safe when traveling grew to tiring. Instead she was stuck in a cell, treated horribly and he was to busy training and going through test to protect her.

He let out a hiccuped cry, eyes growing misty. He slammed his head against the wall, fingers running along the slick tiles. Why was he so pathetic? He couldn't do anything and because of this whole test, the tool he was building was delayed. He had no time to build because he had very little free time. If he did have free time he spent it sleeping, trying to regain his energy for the next inevitable test. He was sick and tired of it all. The only reason he kept going was that he needed to get Donna and all the other prisoners out of here. He couldn't care less about what happened to him, but Donna needed to be safe with her family. Except that would be a difficult task to get her home if they didn't have the TARDIS.

The Doctor lept to his feet, hitting the wall harder. Kicking and punching. Each punch released a bit of tension and anger. He yelled at the wall, cursing the cell, people, this organization, and Earth. No matter how many times he saved this stupid planet, he never got anything in return. No one knew who he was and if they did they wanted him for their own personal agendas. He was sick of it all. The foul treatment, the hate, and fear all because he was born on a different planet. Why did he even bother. Earth could burn for all he cared. He would happily sit back and watch it too. His eyes narrowed and he breathed heavily. He wanted them dead. Every last one of them. He was a Time Lord for Rassilon's sake, he could wipe the stupid apes out with a wave of his hand. Why should he care about what happened to them. He should of let one of those alien invasions wipe Earth out completely a long time ago.

He felt the rage and hatred burn in his hearts. His eyes burned a bright gold. His teeth clenched in fury and frustration. He felt the oncoming storm approach. He wanted to see these humans burn. He would show them what the Daleks were afraid of. What granted him the name Destroyer of Worlds. The Oncoming Storm. What use was the human race anyways. They caused trouble, making wars across the universe as they expanded. Even starting wars with other aliens just so they could take their land and resources. They were stubborn, greedy creatures, who didn't deserve his time or patience. There were plenty of other planets who deserved his protection. Why should he care about the humans?

"Doctor." The concerned voice of Donna reached his ears. "Bobby told me what happened. Are you alright?"

And right then he remembered why he protected Earth. He protected Earth for all his brilliant and loved companions. For Martha, the girl who walked the Earth, saving the human race and all of creation. For Sarah Jane, his oldest and dearest friend, who stuck by his side and put her part into helping the world one step at a time. For the Brigadier, even though they had their fights he was always there, helping the Doctor when he needed it most. For Rose, who pulled him out of the slumps and made him look at the world with child-like wonder again. For Jackie, who took care of him after his regeneration. For Mickey, who willingly left to a parallel Earth to help the humans there defeat the cybermen. For Jack, the immortal man. The ex-time agent who made his home in the 21st century and fight a long battle everyday to protect this tiny blue and green ball. Who suffered through the year that never was. Who was always there to help if he needed it. For Wilf, who dreamed of the stars. For Donna, his best friend and 'partner in crime', with her compassion for all living things, wonder and excitement, and her brilliantly quick tongue she had proven to be the companion he needed most. Someone to make him think about a situation and not react hastily. To look at all the options before making a decision. She thought herself stupid and ordinary, but there was something special about her. Something brilliant. He noticed the little spark from the very beginning, even when it was hidden under her mask of indifference and anger. The more she traveled with him, the more she opened up and that brilliant little spark kept growing.

The Doctor remembered all of his other past companions. The people who willingly put their lives on the line everyday. Who came with him, wanting to discover and learn about the universe. Even now many of his old companions were trying to make Earth a better place. Like Jo Jones and her large family, who travel the world as environment and political activist. Who risk everything to protect the trees. Like Grace Holloway, a doctor working hard to save lives and finding new breakthroughs in surgery that no other would of considered.

He felt the fire inside of him slowly die. His hands unclenched and his breathing slowed. There were so many wonderful people out there, trying to live. Why would he allow a few bad eggs to destroy his morals and beliefs? When out there a whole race of brilliant people lived and a new generation would soon come through just as brilliant.

Yes, he would shut this place down. A place like this should not exist in the universe. He would build his escape tool and he would get everyone out. He didn't know when, but it was going to be soon he hoped. He had people to save. The gold in his eyes slowly died down. He may be known as the Destroyer of Worlds, but he wasn't going to live by that name anymore.

He glanced over at Donna, a worried expression on her face. He smiled reassuringly at her and she raised a brow, crossing her arms. One thing for sure, if he couldn't get out, he was going to get Donna out of here. "I'm alright Donna," he responded, "Just went through a rough patch that's all." Donna's eyebrows shot up to her hairline incredulously, before she squinted her eyes accusingly.

"Is this Time Lord alright," Donna stated, "Because if it is, I'm not taking any of that nonsense Sunshine." The Doctor shook his head and chuckled. He leaned his head back against the wall. He probably should tell her the truth. He didn't want to fill her heart with worry, but according to the expression on her face it was a little too late for that.

"Sort of," he responded. A lump formed in the back of his throat. He didn't want to talk about the incident. It had stolen his pride and confidence, stomped all over it, and tossed it into the filthy gutters of self-doubt. He brushed a hand through his tangled brown hair. His face set solemnly. Donna's features automatically softened and she smiled encouragingly. Every part of her spoke volumes of her compassion and loyalty. She would never make fun of his suffering.

"Go on Spaceman," she said softly, "I'm listening." She sat back, her red hair curling around her ears. Her blue eyes intently watching him, waiting for his story. There was no disgust or pity behind those blue orbs, just friendship and compassion. The Doctor took a deep breath and begun his tale of drugs, humiliation, and a sickness he wished to never face again. Donna listened, never once interrupting.

* * *

**I hope you enjoyed this chapter, It was shorter than usual, but later chapters will be longer. :) I wanted to show the emotional turmoils going on inside the Doctor's mind. I hope I did a good job with that. Throughout this story the Doctor will be bouncing back and forth between these two emotions. So, the emotional turmoil is not over yet. He will be constantly questioning himself and his abilities. :) Thank you again for all your encouraging reviews and I hope you review some more and tell me what you think.**


	25. Chapter 24

**Thank you for all the reviews. :) I'm glad you enjoyed the last chapter. Warning to all who are slightly squeamish, this is slightly gory and painful to read. I think this chapter should be rated M, just because I'm nervous. I just wanted to let you know, but if you made it this far I think you'll be fine. Please review. I love reviews!**

Chapter 24

The Doctor was chained down to another metal table. He was stripped down to his boxers and his chest exposed to the harsh light above. He squinted as the light shone into his sensitive eyes. He squirmed slightly as the heat of the light prickled his raw skin. His eyes shot around the room, taking in the new lab room...or torture chamber as he preferred to call it. A small cart stood next to the table he laid on. On top of the cart surgical tools sat. there were scalpels, scissors, needles, bulldog clamps, forceps, and many others instruments on the cart. A dotted line ran down his abdomen. The Doctor gulped, glancing around the room quickly. Sweat dripped down his face as panic took over. Were they already finish with him? Was this the end of the line? He squirmed a bit more. He wasn't ready to die. He still had to save Donna and all the others. Would he even regenerate when they were through with him or would they find a way to keep him permanently dead?" The Doctor's brown eyes shot around the room in a panic. He noticed other devices hanging on the wall, each one more menacing then the next. He saw shockers and whips and something that looked like iron rods. His eyes widened in terror and his hearts thumped faster against his ribcage. He bit his lip, blood dribbling down his chin.

They had drugged him before dragging him to this room, probably to prepare him for his inevitable fate without him squirming and pleading for mercy. He wasn't normally one to plead, but these last few and a half weeks, at the Underground, had been very trying to his regular reactions to situations. He found himself behaving in ways he would never of considered doing before. Squirming and pleading was one of them. The Doctor took a deep breath, attempting to get his nerves under control. Panic wouldn't help him when the scientists arrived. It would only stress him out more. He took another deep breath, remembering what Dr. Black said about the Colonel wanting to keep him around longer. But people change their minds. He might decide the Doctor was to much trouble to keep and ordered his execution. The Doctor felt the panic rise to his throat. He wanted to scream and protest against this treatment, bu fear kept his mouth shut. He didn't want to make the situation worst. He closed his eyes, counting to ten.

His eyes snapped open to the opening and closing of the door. The loud bang intimidatingly echoed off the walls. Five people entered the room, the loud clatter of feet grew closer to the Doctor's side. The Doctor struggled to keep his breath even, plastering a friendly grin on his face. Underneath the mask he was shaking, scared of what was about to happen. His mind rampaged through every possibility each one growing worst and worst. He knew he was about to be cut open, but he didn't know how far or whether he'd survive the experiment or not. The ugly face of Dr. Carter appeared in his line of sight. Carter's black eyes squinted sinisterly and a cruel smile crawled across his slim face. Grizzly fingers roughly grasped the Doctor's chin, turning his face side to side, hot breath brushing the Doctor's nose.

"How are you doing today, my pet," Dr. Carter asked, brushing his long fingers against the Doctor's cheek. Dr. Black appeared at his other side, her face stone cold. The Doctor coughed slightly, trying to turn his face away from the two mad scientists. But Carter's fingers held his face firmly in place, forcing the Doctor to look at him. Carter squeezed his cheeks hard, staring at him threateningly. "You better answer my question. I don't like disobedience. You've been here long enough to know the consequences." The Doctor stared defiantly up at Carter.

"Never better," He choked out. "Long time no see Dr. Carter. Sorry we haven't had the time to hang out and chat lately, but I've been busy. You're lucky I could book you in today." A cheeky smile appeared on the Doctor's squashed up mouth, his flippant response earned him a shock. He grunted as electricity coursed through his nerves, shattering his pain receptors, and stabbing into his limbs like a thousand needles. The Doctor gasped as the sudden shock ended. He didn't see a guard with a cattle prod. So it must have been something built into the table.

"The manacles you're wearing have a electrodes wired into them, every time you do something I don't like, I press this button..." Carter held out a remote with a dial and a large green button. "Which will give you a powerful shock. Do you understand?" Carter glared threateningly at the Doctor. He must of taken some lessons from Major Johnson.

The Doctor nodded his head, "No flippant responses. Got it. If I could move my hands I would zip my mouth shut, but unfortunately." He jingled his strapped down hands and gave a struggled shrug. Dr. Carter chose to ignore the last bit. He turned away. The Doctor heard the clatters of tools and other objects being placed on the tray. He was not looking forward to this particular test. Not that he ever looked forward to any of the test, but this one in particular gave him the shivers. Dr. Carter stepped back into the Doctor's sight. He held a tray of surgical supplies and other objects that weren't there before.

"Alright lady and gentlemen," Dr. Carter started, " In today's test, we'll be looking at Subject 13's healing factor. How fast he heals depending on the wound." The Doctor gulped, preparing himself for the test. He was not going to scream this time, no matter how much it hurt. He wasn't going to give them the satisfaction of his pain filled wails. "As you can see I drew a dotted line down subject 13's abdomen, after the healing test, we are going to have a little peak at its digestive system. I want to see how its metabolism works and the only way to get a proper peak is to open it up." Dr. Carter grinned. The Doctor gulped. He couldn't promise himself not to scream while he was gutted like a fish. "Any questions?" the room was silent as Carter glanced around, waiting for a question. "No," he questioningly stated, a smirk twisted at the corner of his lips, "Good. Let's begin. Dr. Black would you kindly set up the stopwatch. We're going to see how long it takes for the first wound to close up." Dr. Black grabbed the stopwatch next to the table, holding her thumb over start.

Dr. Black nodded her head. Carter picked up a scalpel and placed it on the Doctor's arm and slowly tore open the flesh. The Doctor gritted his teeth, as blood seeped from the wound. The blood dripped down his arm in a reddish-orange trail, plopping onto the metal table. He felt the regeneration energy slowly flow up to the wound. The skin snapped back into place, mending the opening. Golden light ran across the wound, sparking. Like a tiny fire-cracker it flickered and disappeared. The wound was gone and in its place was smooth, new skin. It was like the Doctor was never even cut.

Dr. Black paused the stopwatch, glancing down at the time. "Nine point five seconds," she stated. Dr. Carter smirked, brushing his hand through the Doctor's hair. The Doctor squirmed a bit under his touch. His long, bony fingers cold. "Fascinating," Dr. Carter mused, "Nine point five seconds for a paper cut length wound to heal. Let's go a little deeper shall we." Dr Carter stabbed the Doctor a few centimeters deeper than before, slowly cutting into his skin once more. A man stood in the back with a clipboard, quickly writing the times down for each cut.

The Doctor gritted his teeth as the scalpel was pulled out of his skin. Dr. Black glanced over at the wound. A bright gold light quickly ran up the Doctor's arm and swallowed it in sparkles. The scientists spotted the skin pulling itself back together and snapping close over the open gap.

"fifteen point seven seconds to heal a four point five centimeter deep cut." Dr. Carter smiled at the announcement.

"Lets go a little deeper than," he suggested. He stabbed the Scalpel deeper into the Doctor's flesh. The Doctor bit back a cry.

* * *

The Doctor was beaten, flogged, electrocuted, burned, and cut all in the name of science. The first few times the wounds had healed quite quickly, but as time went by and the abuse became more violent, his healing factor slowed down as it tried to race from one wound to the next. Sweat dripped down his face as his feet were burned by hot irons. He wasn't going to cry. Nope. He just wasn't. Even if the pain was unbearable. The Doctor gritted his teeth, as the flesh on his feet sizzled away. If this wasn't punishment than what was? He would happily miss a meal to avoid this treatment. A pop was heard as his feet blistered from the red irons. The Doctor bit his tongue, blood pooled in his mouth.

"Alright, that's enough,"was Dr. Carter's sharp order. The man holding the iron stepped back, waiting intently for the next order. The Doctor let a small moan pass his lips, as his feet blistered and boiled from the heat. "Start the stopwatch Dr. Black." Dr. Black clicked a button and all the scientists gathered around the Doctor's feet. The Doctor closed his eyes, grunting in discomfort as someone poked one of his swollen, burnt feet.

"Why isn't it healing," a strained voice asked. A finger poked his foot again. The Doctor growled in anger at the imbeciles. He snapped one big, brown eye open, glaring threateningly.

"Because you idiots," he began, anger spitting from every word. Rage always covered the pain. "You put my body under to much strain. I normally could heal quite quickly if I had the time to recover. But if you haven't noticed most of my skin is dotted in purple bruises and large slash marks because you went from one violent attack to the next, instead of waiting patiently for my first few wounds to heal." The Doctor breathed heavily in both pain and fury. "See what impatience resorts too. Now this wound won't be healing for another forty minutes because my regeneration energy is busy leaping from one wound to the next. It normally goes in order, depending on when the first wound was given and so on, unless I regenerate. If you pay close attention you can see the last few wounds have already healed, while others are in the healing process." he leaned his head back against the table, teeth gritting in pain. His feet burned and prickled, feeling like a hundred hot needles were stabbed randomly into his soles. The scientists gathered around his body, searching for the wounds that were in the process of healing. They spotted a slight spark, that they would of missed if they weren't looking closely.

"Oh there it is," one of the scientists shouted, "Dr. Black get the stopwatch ready." Dr. Black held the stopwatch in her hand as the gold energy shot to the next wound, completely covering it in its golden light. It took five minutes to heal the deeper cut, before it shot off to the next. This wound was a lot deeper than the rest. It had torn through the muscle and touched the bone. The wound was surround by golden energy that stretched into its crevice, pulling the muscle and skin back into place. The healing process took around fifteen minutes. Before going to the next. The Scientists watched in fascination as the gold energy ping-ponged back and forth to each wound. It was true. The wounds healed in order depending on when it was made. The Doctor's skin was back to its original form except for jagged scars that were seen scattered along his body and the reddish-orange blood that still caked his pale skin.

The gold energy finally reached the Doctor's feet. He sighed in relief as the burnt skin began to mend itself. The blisters begun to pop as the gold energy went inside of them and slowly cleaned out the wound, overlapping the burnt skin, and quickly pulling and stretching it back into place. It suck up the burns, leaving it scarred and mended. The process took about thirty minutes, since the hot irons were held against his feet for a long time.

He wiggled his toes as the regeneration flame disappeared. He leaned his head back, giving a relief smile. The pain was horrible, but he dealt with it and proudly didn't scream in agony. He glanced over at the scientists, who were still staring at his body. The Doctor twisted and squirmed in discomfort under the scrutiny. Dr. Carter licked his lips, his eyes wide with wonder. He glanced over at the Doctor, a predatory spark in his black beady eyes. The Doctor seized his squirming and stared back, a lump forming in the back of his throat. "Aren't you full of surprises," Dr. Carter purred. The Doctor gave a weak smile.

"I try to keep everyone on their toes," the Doctor responded, eliciting a nervous laugh. "Keeps things a little more exciting." Dr. Carter grinned dangerously, stepping a little closer to the Time Lord's side.

"I'd like to find out all those little surprises," he stated. His eyes growing darker with every word. "It would be like a treasure hunt, digging up new findings." The Doctor gulped as Dr. Carter moved even closer. He really enjoyed close contact. "I think its time to find a new surprise." Carter held up a scalpel, placing it on top of the Doctor's belly. His beady black eyes glanced back at the Doctor, a twisted grin curving his mouth. "Don't you agree?" The Doctor swallowed heavily, squirming slightly.

"I-I'd r-rather n-not," The Doctor stuttered out. He cleared his voice. "Maybe we should set this date up for another time. I think its too soon." the Doctor pressed close to the metal table, wishing he could mold into the metal. A dark chuckle bubbled out of Carter's mouth.

"But the fun just begun," Carter coldly stated, grinning. The Doctor wriggled, nervously giggling. At least Carter had a sense of humor, even if it was twisted and warped. The other scientists moved closer with other surgical tools in their hands. He closed his eyes, swallowing heavily. This was just like one of those nightmares he had once. This time he wished he could pinch himself awake. He felt the scalpel dig into his abdomen, smoothly cutting into his skin, and opening the wound wider. The Doctor gritted his teeth, sweat spilling down his face.

* * *

The Doctor's face was a ghostly pale. His lips were thin against the background of his skin. His brown eyes were screwed shut, unwilling to look at what the scientists were doing. A pain-filled moan was released from his lips. A scientist was digging through his insides, pushing the intestines around and taking notes. He heard the soft scribble of writing on a pad of paper. A breeze tickled his innards and he felt someone pull something out, possibly part of his gut, and hold it in their hands. The Doctor squealed in pain. He had never been opened up before, so this was definitely a first. He could clearly say he never wanted to go through it again. Blood flowed down his side as the Scientists continued to examine his insides, poking and prodding.

"Subject 13 has more than one stomach. I have counted three," Dr. Black announced, "This explains why its not as vulnerable to malnutrition like many of the other aliens. Humans included. It probably doesn't even need one meal a day. One of these stomachs stores food for later." The Doctor cried out as he felt a rough tug. Why were they doing this to him? Oh, right in the name of science. He never thought he would despise science as much as he did now.

"Oh look at this. This stomach here has the ability to interpret human memory RNA and create its own equivalence," A scientist exclaimed. He gently prodded at the stomach, "I would love to dig further, but I don't want to kill it early. I'll take a look when we do a more thorough dissection." The Doctor screamed, closing his eyes tightly. His bottom lip wobbled.

"I believe its stomachs are able to metabolize normal human foods," Dr. Carter announced, "The lining and development of these stomachs are similar to that of a human's stomach. I think its digestive juices can break down the foreign foods not normally introduced to its diet."

"See how its metabolism is set up," a second scientist exclaimed, "It appears it would be able to digest alcoholic beverages quickly without dealing with the drunken effect afterwords. Basically it can't get drunk." The Doctor moaned at the poking and prodding. He risked a peak, popping an eye open and instantly paled. His intestines and stomachs were hanging out in the open and the scientists were digging through them. Another breeze touched his insides and he shivered. His face turned even paler than before, seeing his insides. His head fell back, smacking the table. He groaned.

"What other little surprises do you have for me, my pet," The Doctor weakly popped an eye open, spotting Dr. Carter's face amongst his insides. He squealed in surprise and distress as more of his insides were moved around.

"p-please d-don't d-disorganize them," the Doctor stuttered out, sweat beading his brow. Dr. Black glanced over at the Doctor, her cold stare slightly softened. Which was a bit of a surprise.

"Don't worry everything will be put back in its rightful place," she responded, before her look hardened once more. "Now answer Dr. Carter's question." The Doctor whimpered, screwing his eyes shut at another tug. His hearts beating fast from the shock. He collected his courage and voice, turning his head back to Carter. He gasped as blood bubbled out of his mouth, tinting his teeth red. A scientist stepped over, wiping his mouth clean. He cleared his throat.

"I c-can c-control my metabolism," he stated, swallowing down a painful lump. " making it impossible for me to get drunk. I can go without food or water for long periods of time, but when forty days have passed, I will n-need f-food..." The lump had returned and the Doctor crowed in pain. Gritting his teeth, he snapped his eyes shut. Dr. Carter nodded his head. Before turning to the other scientists.

"Sadly our time is up," Dr. Carter stated, "Let's put subject 13 back together and stitch it up. I don't believe its healing factor will work quite as quickly this time." The scientists immediately nodded their heads and went to work.

They quickly put the stomachs and intestines back in their rightful places, the Doctor moaning the whole time. His face was speckled with sweat and deathly pale. Blood caked his skin and hair and the table he laid on was soaked. He barely noticed the needle that sewed his wound back together or the gentle tug of the string and needle snapping off. Cold ointment was smoothed out over his stitches, settling the burning pain. He groaned slightly as the chains holding him down were snapped off.

Somebody shook his shoulders and the Doctor's eyes snapped open. Dr. Carter was standing next to him. "I think subject 13 will need a clean up, before heading to the training room," Dr. Carter stated. The Doctor groaned at the thought of training with Major Johnson. "It smells like blood and sweat."

Two of the scientists nodded their heads and walked forward. They lifted the Doctor off the table, steadying him. His knees were weak and he kept collapsing to the ground. The scientists had to use their full strength to hold him up. The Doctor's head bent backwards and a gurgled cry released from his throat. The two scientists walked him over to a small room in the back where a shower head hung from the ceiling. One of the scientists switched on the water and nice cool water spilled over the Doctor's face.

The Doctor closed his eyes contently. This was the first actual shower he had in a long time and it felt wonderful. He leaned against the scientist on his right, as the one on his left pulled out a shampoo bottle and squirted the sticky soap into the Doctor's brown hair. The scientist scrubbed the shampoo into his scalp and flakes of blood washed away. He watched as blood and grime swirled into the drain. The shampoo washed over his body, cleaning the dirty skin. His legs wobbled slightly from the weight. The scientists held him up, making sure he didn't collapse before dragging him out of the shower room. One pulled out a towel and quickly helped him dry off, before pulling out fresh clothes. They helped him dress, before slowly leading him back to Carter, Black, and the remaining scientist. The Doctor slightly tilted his head to the two scientists holding him up.

"T-thank y-you," he whispered hoarsely. The scientists nodded in response. Two guards walked out of the shadows, quickly taking hold of the Doctor's arms. They carefully led him out of the lab and down towards the training room. Hopefully, Major Johnson would take pity on his condition and give him a break.

* * *

**Thank you so much for all the reviews. I know this chapter was a little shocking and I felt terrible writing it, but I had to squeeze into the minds of uncaring, psychopathic humans. Trust me, I had a hard time writing this. Some to most of the stuff I've mentioned is somewhat accurate to Time Lord biology. I found a lot of the information on sites that dedicate their time in breaking apart Doctor Who literature and shows to give an accurate idea of how a time lord works. If the information is vague I may exaggerate a little or put my own ideas in on how something works. The metabolism information is all true or somewhat true. I couldn't find how many stomachs a time lord has because the site just gave stomachs. In this story he has three. :)On another note, I am planning to do some mental test. So, I may need ideas. I have a couple, but more would be wonderful. :) I might Rte this story M, What do you think? I don't know if I'm being paranoid or not. So, yeah need some advice. Thank you again for all the reviews and I hope you review some more. I will try to update tomorrow. :)**


	26. Chapter 25

**Thank you for all the reviews. I know the last chapter was intense and some may not of read the whole thing, so I'm going to give you a recap of what they discovered about his metabolism.**

**The Doctor has three stomachs, one is the normal digestive track that all aliens and humans alike have , the second stomach: can recreate human RNA and create an equivalence to Gallifreyans, the third stomach is more of a food pouch that stores nutrients for later if a time lord hasn't eaten in a while. This also helps him avoid malnutrition. All three can take turns in digesting food or storing foods. This is just what they mainly do. **

**The Doctor can go without food for 40 days, anything past that he would become delirious. Also the Doctor only needs to eat once everyday**

**The Doctor can metabolize alcohol extremely well. Basically he can't get drunk**

**The Doctor can control his metabolism. He can also digest just about any foreign food without problems. **

**If you didn't read the healing factor part, basically the Doctor can heal really fast and the regeneration energy goes in order from the first wound that is created to the last. **

**So, there is my recap of the last chapter to all who didn't read it. This chapter is pretty mellow comparably. Basically Donna comforts Doctor and other stuff. Hope you enjoy this chapter and please review. I love reviews!:)**

Chapter 25

"Get up!" Major Johnson ordered. The Doctor laid sprawling on the ground, his cheek rested against the cold floor. Everything hurt. His abdomen hurt. His legs hurt. His head hurt. Even parts that normally didn't hurt felt like it was wallowing in pain. His hair was still dripping wet. He had only been training with Major Johnson for around thirty minutes before his legs finally gave out. He really wasn't trying to be rebellious, he just couldn't move. But apparently his painful collapse and moan was to hard for the Major to read into. The Doctor, before his fateful collapse, was in the process of a hand to hand combat fight with the Major. He was doing well, slower than he normally was but he was still able to throw in a couple blows. Combat training was normally the first hour warm-up they started with, followed by weapons training and obstacle courses. Today the plan was a lesson in breaking into buildings or safes without being detected. Which was easy enough in the Doctor's opinion. He did it on a regular basis. But the Major gave one blow to his abdomen and he crumbled. He didn't collapse right away, he stumbled about trying to gain his footing, before his knees gave out. He was to tired to climb back to his feet.

"Get up now," the Major ordered, spittle flying from his mouth. A vein in the Major's neck pulsed. Spit smacked the Doctor's face, but he couldn't move his arms to wipe it away. "Or you will be punished for your disobedience." The Doctor glanced up at the Major, glaring. He was angry. Scratch that...He was furious. If looks could kill the Major would be a tiny pile of dust right now. The Doctor gritted his teeth, he was so tired of this treatment.

"I can't you moron," the Doctor acidly retorted. He didn't care if he was punished for his response. If he couldn't move, he couldn't move. "I can barely move my head and whatever punishment you have planned is nothing worst than what I just went through." The Major glared threateningly at the Doctor, his fingers twitching at his side.

"What did you say to me," he growled. His eyes burnt with hate. The Doctor's eyes widened, he wouldn't hold it against the Major to beat him senseless for his response. But the Doctor didn't care, his eyes squinted in defiance.

"You heard me," the Doctor acidly stated, "I don't care to repeat myself." He braced himself for punishment. He closed his eyes and his muscles tensed with anticipation. But the blow never came. The Doctor risked a peak at the Major. Johnson loomed over him, his arms crossed.

"I don't like your attitude," the Major snarled. His arms loosening, falling to his side. He got down on one knee next to the Doctor. He reached a hand out and the Doctor slightly flinched. He lifted the Doctor's shirt, to expose the stitched up opening from his ribcage down to his intestinal area. The wound was slightly opened and blood was dripping out because of the blow. The Major pulled the shirt back down, growling. He stood up, pulling out a communicator.

"Can you please send a medic down here immediately," the Major ordered, "Subject 13 needs medical attention now." A quick 'yes sir' was heard from the other end before the comm. link was shut down. The Major turned back to the Doctor. The Doctor's grayish-white shirt was already colored with blood. He gasped, squirming as the pain became worst. The Major rubbed his mouth, watching the Doctor wriggle on the ground.

"Damn," he hissed. He turned around and banged his fist against the wall. "Stupid scientists messing up my training." He turned back to watch the Time Lord. Johnson hadn't realized the injuries extent until now. The Guards were extremely vague about what occurred before hand, but obviously Carter decided to slice open the alien for his own purposes and forgot to discuss his plans with Major Johnson. Now the Major was forced to deal with an alien bleeding out on the training room floor. Damn.

The door to the training room opened and the soft clips of feet vibrated off the ground. The young physician, who had dealt with the Doctor's werewolf injuries, entered the room. Her black hair was pulled back into a ponytail and her green eyes widened in shock when she spotted the Doctor. She immediately fell to her knees and opened up the medical kit.

"What happened,"she asked professionally, her tan face turned towards the Major. She held a needle in her hand and slowly filled it up with a clear liquid. The Doctor's struggled gasps, was the only sound made in the room for a while. He watched warily as the medic prepped the needle. She noticed his look and her gaze softened. "Don't worry," she whispered to him, "Its just a pain-killer." The Doctor nodded his head, wincing slightly.

"Aspirin?" he asked nervously. The young physician shook her head.

"No," she responded, "We've found out that a lot of aliens react badly to aspirin. The scientists have created a new pain-killer." The Doctor coughed and a needle was plunged into his skin. The needle was pulled gently out. His eyes drooped drowsily as the pain disappeared.

"Thank you," he stated. The Physician was pulling out surgical suture and a needle. "What's your name?" The physician smiled softly, trying to keep him calm.

"Claire," she answered, "Why do you ask?" The Doctor shrugged, yawning. He turned his head and glanced at Claire lazily.

"I just wanted to know the name of the woman who's stitching me up," the Doctor stated with a smirk, "And who helped me last time with the werewolf injuries." She gave a shy smile, before putting the suture through the needle.

"This might sting a bit," she warned. The Doctor shrugged indifferently. The needle plunged into his sore abdomen as she begun to close the wound once more. The Doctor screwed his eyes shut, pursing his lips. She cut the extra bit off and quickly pulled out a large white bandage. She smoothed it out over the stitches, before packing away her medical supplies. "There we go, good as new," she stated. She turned a fiery gaze back at the Major and crossed her arms. "Now would you like to explain what happened," she repeated, "I thought I gave you a warning about overworking subject 13." The Major sneered at the young lady, but her glare hardened. "I'm waiting." The Major crossed his arms, clearing his voice.

"Subject 13 was sent to me for training today," he started, "But the scientists, specifically Dr. Carter, forgot to mention their little experiment. I was going through warm-ups with it, when I punched it in the stomach. I didn't realize at the time that subject 13 was seriously injured, so when it collapsed I thought it was being defiant. I noticed blood spotting its shirt and took a peak, finding that its stitches had ripped open. That's when I called for a medic." Claire nodded her head, before picking up the bag. She handed the Major a bottle.

"Those are pain killers," she stated. The Major glanced at the bottle. "The pills are laced with antibiotics. I want these given to subject 13 twice everyday until this wound is healed. I don't want subject 13 training for a few days. It needs to to relax. I don't want to deal with a repeat of this situation. Let it rest and I believe it'll be good as new in no time. I'm going to talk to the scientists now." She turned on her heels and marched out of the room, medical bag in hand. The Major turned to the Doctor. His breathing had slowed down and he looked drowsy. The Major marched over, pocketing the bottle.

"Come on subject 13," he stated. He placed his arms around the Doctor's waist and slowly lifted him to his feet. The Doctor leaned his head back, resting it against the Major's shoulder. The Major grunted from the weight and slowly walked the Doctor back to the cellblock, "Lets get you back to your cell." With a struggled slow pace, they headed out the door, and down the hall.

* * *

Donna lept from her bunk when she hear the doors open. Ama, the Shian, had tried to keep her from worrying but it was no use, she was a nervous wreck. She spotted Major Johnson holding up a crumpled figure. The Doctor. Donna gasped and immediately she felt her face heat up.

"What did you do to him!" she shouted, banging a fist against the wall. "You better answer me!" The Major ignored the fiery tempered woman, instead opening the Doctor's cell and carefully leading him over to the bunk. The Doctor immediately collapsed.

"Oi, I'm talking to you sunshine!" Donna yelled, "Your lucky I'm behind this force-field because you would be picking up your scattered remains, buster! Do you hear me!" Donna kicked the wall, before taking a worried glance over at the exhausted Doctor. The Major glared at Donna.

"You better watch your mouth freak," he stated coldly, "You might find yourself dead one day." Donna's mouth gaped and she squinted her eyes dangerously.

"Did you just threaten me," Donna hissed, "I don't take threats to kindly." The Major turned away and marched down the hall.

"You must be bored," he said threateningly, "I might find a way to make you useful. In the meantime watch your back." The door slammed shut as the Major made his exit.

"SLIMEBALL!" Donna shouted at the door, stomping her foot. She huffed angrily, flicking her hair back. The Doctor laid unconscious in his cell.

"Poor Spaceman," she whispered, "He doesn't deserve any of this." She leaned back, watching the Doctor sleep. He deserved the rest. While the Doctor was absent, Donna was slowly organizing all the prisoners. Trying to find the best way for everyone to escape. She decided Roctarus would exit first since his rock form was indestructible. He could shield everyone from the darts and other traps. Ama would go second, providing a telepathic covering for all of them. She would also be able to manipulate the guards minds, sending them in opposite directions. Then the Doctor would exit next, along with her. He would dismember the traps and get everyone out. The rest of the aliens would trail behind, using their abilities when they were needed. She knew there were other aliens in the Underground and knowing the Doctor he would probably find and release them. She just hadn't figured out how he would manage that. So, she left that part of the plan up to him. They had discussed escape countless of times, but right now it seemed more of a hope than reality.

But Donna didn't want to push him. He was already exhausted enough, trying to push through the tests and training exercises. She was confident they would escape, they always did but she just didn't know when. To pass the time, she spent her hours perfecting the plan. Her last trip out of her cell was meeting the Colonel. She had payed close attention to the halls she walked down, but the place was like a maze. There were twist and turns around every corner and she was lucky spotting at least a couple exits. But she didn't know where those exits would lead too. She glanced over at the Doctor. He was tossing and turning on the bunk, groaning in discomfort. His hands clutched his abdomen. Donna sighed. Spaceman didn't need this treatment, he had enough on those skinny shoulders of his.

"Its ok Doctor," she whispered comfortingly, "I'm right here." Tears prickled at her eyes. This place was horrible. She had never seen the Doctor look so defeated before. Here she had witnessed that posture of defeat from him too many times to count. She sniffed, refusing to crumble. She had to be the anchor here. To hold the Doctor in place and keep him confident and faithful in his abilities. She was scared that his normal confidence was fading. That he would soon bend to these humans expectations. She shook her head, running her hand over her mouth. He was stronger than that, she knew it. He would never follow these people and their rules. What was she worried about?

The Doctor let out a strangled cry and Donna covered her mouth. Hot tears rolled down her cheeks. "Spaceman I'm here," she whispered soothingly. What had they done to him? The Doctor's eyes snapped open and he thrust himself off the bed, groaning from the sudden reaction. He leaned back panting, sweat dripping down his brow. His face was a ghostly pale and his normally exuberant brown eyes were cold and haunted. He turned his head over to Donna. Donna wiped at her face, trying to hide the tears. The Doctor smiled reassuringly.

"Why are you crying," the Doctor asked, his eyes softened. Donna shook her head.

"I'm not crying," she retorted indignantly, "I have something in my eye." The Doctor raised an eyebrow.

"Sure you do," he responded, rolling to his feet, gasping. He clutched his abdomen and sat back down on the bunk. "What's wrong?"

"Nothing," she said defensively. "I should be asking you that question." The Doctor shrugged, leaning his head against the wall.

"Suit yourself,"he responded, "You know there is nothing wrong about exchanging feelings." He glanced over at Donna. Her fist balled and jaw set, she wasn't going to budge. The Doctor plastered a smile on his face. "Maybe if you tell me what's wrong. I can tell you what happened to me." He shot a glance over at Donna, her features had softened slightly and she was leaning against the wall defeated.

"Ahhh," he said, "I see." Donna glared at the Doctor.

"See what," she asked. She crossed her arms, her blue orbs watching his every move.

"The issue,"The Doctor stated, "do you want to talk about it?" He looked at his nails and picked away the blood that was still present. Donna slumped. She played with her red hair, watching the strands twirl.

"I mind as well,"she stated in fake exasperation. She glanced over at the Doctor, who watched her intently. She sighed. "You never give up do you,Spaceman?"

"Nope," he stated popping the p, "Never. Now tell me what's wrong." Donna glanced back at the red strand she twirled around her finger. She felt the tears prickle at her eyes once more.

"I have nothing to complain about. Nothing to your extent anyways," she stated. She felt her bottom lip wobble, trying to hold back the emotions. "I am so tired of trying to be brave," she admitted, "I want to protect you but I can't and I-I c-can't handle it." The Doctor nodded his head in understanding. "I am just a weak, stupid human. I try to organize everyone but I seem to fail." Tears spilled from her eyes. "Look at me,"she announced, "I'm a freakin' water fountain. I was going to comfort you and let you know I'm fine...But." Donna sobbed. She was tired of the fear. Being scared about what shape the Doctor would be in when she saw him next. She wanted to help everyone. Get everyone to safety but that plan had been delayed. She was just scared. Scared of what the future would hold. Will she even be around in the future or will she be dead and the Doctor alone? She couldn't handle not knowing. The Doctor watched Donna sob, his hearts ripping into shreds. This was what he wanted to prevent. Donna never gave up and here she was on the brink of calling quits. He felt the emotional lump form once more, choking him.

"D-Donna I'm so sorry," he stated, tears forming. Donna wiped her eyes.

"Why are you sorry," she asked, "You have nothing to feel guilty about."

"I brought you into this mess," the Doctor responded, "If I didn't stop off at Cardiff that day things would be..."

"Still the same," she interrupted, "They would've found a way to get you eventually. Doctor look at it this way, if we weren't captured we wouldn't of found all these people trapped down here. There's a reason why we're here. Ok?" The Doctor nodded his head, tears trailing down his cheeks. He couldn't protect her or anyone else. He had never felt so vulnerable before.

"I-I'm s-sorry," he stuttered. He buried his face into his hands, sobs shaking his body.

"Spaceman, It's ok," Donna responded, "I don't blame you. I'm angry and frustrated at this place but I'm not mad at you. You've nothing to feel ashamed about. This is not your fault."

"Yes it is," He stated, "All of this is my fault. I am weak and can't protect anyone. I didn't even know this place existed until now. If I did it would be gone."

"How would that be your fault, Spaceman," Donna asked reasonably, "That is the poorest excuse for guilt I have ever heard."

"It just is Donna," He bit back angrily. "Everything's my fault." He laid down on his bunk, mumbling in Gallifreyan.

"Major guilt complex much," Donna retorted back, her features softened, "Spaceman what happened?" Her eyes were still puffy from crying, but she decided it was her time to take the reigns of this conversation.

"I don't want to talk about it," the Doctor mumbled into the thin mattress. Donna could barely pick up the response.

"Well you're going to have to talk about it," Donna said calmly back. Her worried eyes watched. "We made a deal." The Doctor moved around on the bunk, a pair of pain-filled brown eyes looked back at her. He slowly got up to his feet and stepped over to the force-field. His arm wrapped around his abdomen.

"Do y-you r-really w-want to know," he asked, eyes red. Donna nodded her head. The Doctor sighed and lifted up his shirt. A long scar ran down his abdomen, swollen and infected. Donna covered her mouth, leaning against the wall. "T-they c-cut me open. W-wanted to see my m-metabolism at work. They also t-tested my h-healing factor." Donna's face turned pale, tears threatening to spill once more.

"I'm sorry," she responded, "I didn't know." The Doctor shrugged his shoulders and sauntered back over to his bunk.

"How would you of known, Donna," the Doctor stated. He laid down on the bed, "The only good thing that came out of this is that I get a few days to rest. No tests or training. I can focus on healing and building the escape tool." Donna nodded her head, hand still covering her mouth in shock. She couldn't remove her eyes from the Doctor's abdomen. "I'm going to get some rest," The Doctor stated, "go into a healing coma. I need to try and fix this mess up." His hand gestured to his abdomen. "Wake me up when supper comes around." Donna nodded her head. The Doctor closed his eyes and fell asleep.

Donna watched, leaning her head against the white-tiled wall. "I'm so sorry, Spaceman."

* * *

**I hope you enjoyed that chapter. The next chapter will also be a Doctor and Donna cell scene, before we head into the next test. Which will be a mental test. Thank you again for all the reviews and I'll update soon. Please review some more. :)**


	27. Chapter 26

**Hey everyone, thanks for the reviews. :) Here's the next chapter...like you didn't know. ;) I hope you enjoy and please tell me what you think. Thank you. :)**

Chapter 26

The Doctor lounged against the far wall of his cell, contraption in hand. He used a screwdriver to tighten a few of the bolts that he snagged from other electronics he was given. Surprisingly some of the other prisoners, when they left their cells, got hold of materials for his escape tool and stuffed them under their shirts as they were brought to different lab rooms. When they arrived back to their cells, they would sneakily roll it under the forcefield towards the Doctor, winking in reassurance. It seemed everyone was putting their full effort into escaping. The cell block actually buzzed with excitement for once at the prospect of escape. The Doctor, as promised, hadn't been dragged to any of the labs or training rooms for at least three days and because of that his stitches had basically fallen out and his wound almost healed. He was able to get some sleep in, but the majority of the time he was building and preparing for their escape. He knew it would only be a few more days before his plan could be put into action.

The alien prisoners seemed to have a code language between them that the employees at the Underground couldn't understand. They had alerted the other cellblocks to the plan and were apparently met with excitement. The other cellblocks were eager to help and offered their assistance when the time came. The Doctor twisted another screw in before smacking the contraption slightly. He glanced over at Donna, who sat on the bunk in her own cell. She stared absently at the wall deep in thought. The Doctor softly smiled. He wouldn't of been able to organize everyone without her. She was the main reason that this escape was possible. She had kept his hopes up and while he was gone spoke to all the prisoners, giving them faith as well. She blinked her eyes rapidly before swerving her head towards the Doctor. Her blue eyes watched his careful movements as he put another piece together.

"Spaceman," Donna exclaimed. The Doctor glanced up from his work, hearing his name. He gave her an easy smile and put down his tools. He sauntered over to the forcefield.

"Yeah," he asked. His hand shot up to his hair, ruffling it. He raised an eyebrow in curiosity, noticing the worry on Donna's face.

"I don't know which exits to take when escaping the Underground," she stated, "I paid close attention that one time. But there was just too many twist and turns to keep track of. I'm sorry." Donna glanced down at the floor disappointed in herself. The Doctor waved his hand indifferently.

"Don't worry about it," he responded, "I can easily get the information and give it to you. When the next guard comes I'll just pick through his mind and grab what I need." He turned away and sat back down. He placed the metal monstrosity back on his lap. At the moment, the tool looked like some metal monster barfed allover it. It was disorganized and random. But the Doctor claimed it would work. He said he just needed to snip a few parts off and put some batteries in and it would work in no time.

Donna shot her head up, glaring. "Pick their brains," she hissed, a little frustrated. Bad food, worry, and little sleep had taken a toll on her temperament. She found herself getting irritated at some of the most ridiculous things. "for information. Why didn't you suggest this before, Spaceman? It could of saved us a world of pain and stress." She harrumphed and kicked her feet out angrily, giving the Doctor the evil eye.

The Doctor rolled his eyes, measuring out some wiring before placing it on the contraption. "Because Donna," he begun, "If you haven't forgotten, since our arrival I've been put through excruciatingly painful tests. I didn't have the mentality or ability to focus on getting the information and most of the time, when I was back in my cell, I was sleeping. Just these last few days I have been able to focus and get my mind back into the game." Donna glanced down guiltily at the floor. She didn't mean to be harsh and the Doctor was trying his hardest to set up the escape plan. She sighed, massaging her temple.

"I'm sorry, spaceman,"she responded. "I shouldn't of snapped at you. I'm just really tired and my patience is wearing thin." The Doctor shrugged, his eyes still focused on the contraption.

"Its fine," the Doctor answered back, "I understand." He heard the door slam open and the loud shouts and hoots of three men he wished to never deal with again. "I think the information will be gained a lot sooner than I expected," he muttered. He quickly rose to his feet and bent down putting his invention, under the bed, into the hole. He leaned against the wall, watching Norris, Benson, and Wells shouting and swinging their cattle prods around. Norris was the ring leader of the group and initiated many of the emotional and physical attacks against the helpless alien prisoners. While Benson and Wells normally just watched and chanted, sometimes even joining in if the meat was fresh. The Doctor crossed his arms and glared at the three men. They had disrupted the peace in the cellblock and immediately many of the alien prisoners had moved into a corner of their cells. They didn't want to be spotted and become the next victim of the guards humiliating torment.

"Good Morning Freaks," Norris greeted obnoxiously. His light brown hair bouncing as he cockily strode to the middle of the hall, Benson and Wells following his every step. "Guess what day it is?" He glanced around a malicious smile set on his face, "Its the monthly 'Play with Norris Day'. Where you spend some time with Norris and his friends." He stated condescendingly. He spoke to the aliens as if he were speaking to children. "Who wants to go first?" Norris searched the cells, waiting for an answer, but everyone kept quiet, cowering in their corners. "No volunteers. No one wants to spend some time with me," Norris asked in a hurt voice. He put his hand to his heart and mockingly gasped.

The Doctor rolled his eyes at the guard's antics. It was now or never. The Doctor's eyes glazed over slightly as he focused on entering Norris's mind, as the arrogant prat ranted. The Doctor glided into Norris's mind with practiced ease. The guard's mind was an open book, all his thoughts were at the surface and none of the doors to his conscience were closed. Apparently, he didn't expect someone to enter his mind. Norris's mind was a jumble of thoughts and memories all tossed in corners or smeared against the walls of his conscience.

The Doctor passed one door. He politely closed it as he heard a man screaming at a young boy and the loud smack and crash as someone fell. The Doctor cringed. He knew the memory was from Norris's childhood. The Doctor continued his gentle pace along the memory path. He saw Norris bullying kids on the playground, him dropping out of school, his mother dying, him joining a gang before joining the military, and entering the Underground as an employee. The Doctor found the door he was looking for. He gently opened the door, careful not to alert Norris to his presence as he entered the memory. It was the whole layout of the organization. Every exit, every turn, twist, route change, and stairwell it took to escape the building. He decided the best exit would be the stairwell that was a few hallways down from their cell. It went straight up and out into a parking lot. He would give the information to Donna when the guards left.

Before leaving, He decided to peak around a bit more. He learned where the other prisoners were held as he gracefully lept from one memory to the next, absorbing all the information he needed. He learned the only way someone could exit a cell block or the building itself was through voice activation. Also the control room was a story up. It regulated the surveillance cameras, the traps, and the cell blocks. He knew when their escape came, he would need to go there and shut down the systems. He noticed a door that was securely locked. Written across the door was pathogen lab. He pulled on it, hoping it would open. But that little tug alerted Norris to his presence. The walls darkened and distressed thoughts passed through Norris's mind about an invader.

The Doctor quickly ran away from the growing darkness, jumping out of Norris's conscience, information still in his head. His mind shot back into his body and he blinked rapidly. The cries of someone in distress was the first sound the Doctor heard. The Doctor shook his head, glancing around. His face burned with anger when he spotted who was being assaulted. Ama. The young Shian was laying on the floor with Norris stabbing her with his cattle prod.

"You entered my mind, didn't you freak," he howled in anger. Ama cried out in agony as electricity ripped through her nerves. "You and your freakish telepathic abilities. I thought they tagged you but apparently I was wrong." He kicked her in the guts, her long white hair curtaining her face.

"I didn't enter your mind," she pleaded, tears rolling down her blue cheeks. "I can't. They have me tagged. Please stop." She rolled onto her side, tears plopping onto the ground.

"You want me to stop," Norris mocked, "Well I'm not, alien. You entered my mind and I know that because you're the only freak here with telepathic abilities." He gave another hardy kick to Ama's side and she howled in pain, curling in on herself. The Doctor felt his face flush with guilt and anger. Ama was being blamed for his actions and he wasn't going to stand for it. He closed his eyes, clearing his throat, before glancing over at the hooting men.

"She didn't enter your mind," the Doctor shouted. The three men stopped their hooting and turned to face the Doctor. Norris kicked Ama one last time before cockily striding over to the Doctor's cell.

"Well, well, well," he started, "If it isn't my favorite smart-alec alien. May I ask why you're interrupting my fun?" The Doctor glared at Norris's condescending words, crossing his arms. Norris sneered at the Doctor. "You better answer my question freak."

Donna watched startled. She had been yelling and cursing the whole time, Norris was beating Ama. She also tried to keep Norris distracted from the Doctor's little dive into his mind. But right now things weren't looking good. Please don't do anything stupid, Spaceman. She didn't know if his body could handle anymore abuse so soon. She knew he would do something like this though, once he realized what was going on. It was inevitable.

"Because you're beating an innocent woman for your own sick pleasures," the Doctor responded back evenly, "You're nothing but a coward Norris, feeding off the pain of others." Donna closed her eyes. Great going, Spaceman. She knew he was trying to replace Ama, so he would get the punishment instead of her.

"Don't you dare talk to me that way freak," Norris growled. Benson and Wells stood behind watching the confrontation. Benson squirming slightly under the even gaze of the Time Lord. Ama laid gasping on the floor, hot tears rolling down her cheeks. "I am your superior and I deserve your respect." The Doctor gritted his teeth, a forced smile spreading across his face.

"I thought I told you last time I don't respect cowards who bully the innocent," the Doctor replied evenly. He cocked his head to the side. "Why don't you pick on someone who is truly guilty." Donna's eyes widened and she swiveled her head in the Doctor's direction. His eyes steady as he stared down Norris.

"Spaceman," she shouted, "Don't provoke him, you bloody idiot." She didn't want to see Ama hurt, but she was more scared about the Doctor being injured. She didn't want to witness him being beaten and humiliated.

"Donna," he growled, warning her to back away. He didn't want her involved in this. He gave her a pleading look. A look asking her to back down for once. Donna immediately shut her mouth.

"You think you're so tough. Don't ya alien," Norris sneered, "Maybe we'll see just how tough you are when I'm through with you. Put the blue freak away Wells." Norris shut down the force field to the Doctor's cell and immediately yanked him out, wielding his cattle prod. The Doctor stumbled slightly, before standing steadily. He refused to fight Norris. He decided to play the role of the weak alien, who's more talk then action. It would keep the idiot from attacking any of the other prisoners, focusing all his rage at the Doctor. He was sacrificing himself to keep Ama, Donna, and the others safe. He took a quick glance over at Ama to make sure she was ok. Their eyes met and she nodded her head, thanking him. The Doctor winked in response, before swiveling his head back to Norris. Benson and Wells grabbed the Doctor's arms, holding him still. The Doctor held his chin high, he wasn't going to scream. He'd been through worst these last seven weeks and he wasn't going to give them what they were looking for.

Norris drove the first punch into the Doctor's solar plexus. The Doctor bent over, gasping for air. A cruel smile twisted Norris's lips as he watched the Doctor gasps for breath. Donna screamed in rage, punching the walls and calling Norris every name she could think of.

"Not so tough now," he growled into the Doctor's ears, "Are you freak." The Doctor glanced up, smiling manically.

"I think a few more rounds might make me crumble," he replied sarcastically, "Your punches are pretty weak. I'd be surprised if they caused any bruising." Norris snarled, punching the Doctor across the face, blood dribbled from his lip.

* * *

The Doctor laid on the ground as another kick drove into his guts. The left side of his face was swollen with purple bruises and three of his ribs felt fractured. He really hated steel-toed boots. The sounds around him was nothing but a noisy buzz. Gritting his teeth, electricity shot threw his pain receptors, feeling like a thousand needles were plunged into his skin. He didn't scream, just took it, allowing a couple flippant responses during pauses. He could hear Donna's voice calling the men every rude word she new, a colorful train of cuss words exiting her mouth. One of the men turned around and shouted at her as one word hit a sore spot.

"Why don't you make me," He heard her shout. A loud bang and grunt was heard as Donna kicked the man who threatened her. The Doctor couldn't focus on anything else, except fighting off the pain.

Norris grabbed a fistful of his hair, yanking his head backwards. Hot breath brushed his nose as Norris stared him down. Blood dripped from his mouth and nose, his face was covered in bruises. The Doctor gave a cheeky smile, his teeth tinted with blood.

"What?" he asked, "finished already? I thought that was a warm-up." Norris growled and slammed his face into the ground. Maybe it wasn't a good idea to aggravate the ego-maniac. He glanced hazily up at the Guards who were all standing around him. Wells was bent awkwardly and had a pained look on his face. Apparently, he was Donna's victim. He also sported a hand-print slap mark across his face. The Doctor couldn't help but smile, chuckling under his breath. He coughed slightly as another kick was driven into his gut.

"had enough," Norris snarled, he twirled his cattle prod threateningly. The Doctor glared up about to respond, but someone interrupted him.

"WHAT THE HELL IS GOING ON IN HERE?" a familiar voice shouted. Jake came stomping through the doors, his eyes commanding and cold. He glanced down at the Doctor, who gave a blood covered smile back. The Doctor's arm was wrapped around his torso. Jake glared threateningly at the three guards. " why are you in here, destroying Underground property," he hissed, "were you given permission to punish subject 13." The three guards stiffened under the scrutiny, looking between each other nervously.

"No sir," Benson stated. He glanced down at his feet. Norris stepped forward and met Jake's eyes, a cocky smirk twitching on his face.

"Simmonds, sir. We were provoked," He lied, "We weren't doing anything wrong, just checking on the aliens and the freak here." Norris pointed down at the Doctor. "Threatened me. I don't take to kindly to threats, so I had to punish it. Make sure it didn't threaten to hurt anyone again." Norris gave an innocent smile. Jake scowled back, his eyes darting to the guilty faces of Wells and Benson.

"Is that so,"Jake asked. The two other guards nodded their heads in affirmation. Jake glared, before pointing to the door. "Get out of my sight." The three guards quickly stumbled out of the room. Norris glanced back at the Doctor, smiling before exiting the room as well.

Jake's glare quickly softened as he bent down to help the Doctor up. "What did you do?" he asked concerned. The Doctor laughed, coughing up some blood.

"Let's say I insulted their egos a tiny bit," he responded. His voice hoarse. "They were beating up a friend and I wasn't too pleased." Jake helped the Doctor back to his cell and rolled his eyes.

"You shouldn't throw yourself into danger," he responded, "You're lucky I arrived here when I did." The Doctor shrugged his shoulders, waving unconcernedly.

"That's what I keep telling him," Donna sharply stated, "He needs to stay healthy and save his strength. Instead of poking at idiots." Donna glared, though her glare was more based on worry then actual anger.

"You didn't have to stand up for me," Ama whispered back, "I could of taken the accusation and punishment myself." Her whitish hair curtained her blue face, a purple eye peaking out from behind. The Doctor smiled.

"I wanted too," the Doctor responded, "I didn't want you to take the blame for something you didn't do."

"How do you know I didn't do it," Ama replied challengingly. Her eyebrow was raised in a questioning manner.

_Because I did it_, he thought back at her. Ama gasped in surprise and a soft smile played at her lips. Even though she couldn't answer back, thanks to the metal tagging, it was still nice knowing another telepath was here. She nodded her head and winked before leaning back against her bed. Donna watched the confrontation between the Doctor and Ama, knowing exactly what he did to make her smile. She stared back at her spaceman, who was slumping on the bunk while Jake tried to get him comfortable.

"Jake," Donna asked. Jake turned his head. "Can you let me out of my cell, so I can see him?" Jake glanced around worried, before nodding his head. He quickly closed up the Doctor's cell and let Donna out. If the surveillance team asks, he'd tell them that Donna was trained in first aid. He led her out and she whispered a 'thank you' in his ear. He opened up the Doctor's cell and Donna immediately ran over to the Doctor, hugging him. The Doctor smiled and wrapped his long arms around her waist.

"Hey there," he said. Donna smiled, staring into his eyes.

"Hey, yourself,"she responded. She kissed him on the cheek. "I was so scared,"she whispered, "I needed to check if you were ok." The Doctor nodded, grunting softly as he sat up. Donna helped him up. He leaned against the wall, grinning. Donna sat next to him, running her fingers softly over his bruises, her eyes growing misty. The Doctor spotted the bruise, forming on her own cheek and immediately ran his thumb over it.

"Did Wells hit you," he asked, rage burning in his chest. The familiar murderous wishes began forming in his mind once more. Donna shrugged her shoulders, wrapping her arms gently around his torso, she didn't want to irritate the wounds. Luckily, his wound from the vivasection didn't reopen.

"He recieved worst," she responded indifferently, "He'll have a hand shape bruise on his face for at least a week and won't be able to walk straight for at least a couple more." she gave a small smirk. "Thanks to my calculated kick." The Doctor smiled amused.

"Fiery ginger goddess," he retorted. Donna gently smacked him on the arm, aware of his injuries.

"Oh, shut-up you," she responded, blushing slightly at the nickname. The Doctor's eyes grew grim and he turned to Donna.

"On a more serious note," he stated, "I need to give you the map of the building. I found the exit we need to take when escaping." She nodded her head.

"Good, good," she replied, "What is it?" Donna glanced up at the Doctor's face, pushing her red hair back.

"I can't tell you," he stated, "I have to show you." He placed his thumbs against her temples, closing his eyes. "Just relax," he whispered. Donna breathed in deeply, closing her eyes as well. Information she didn't have before, spilled into her mind rapidly. She knew each turn to take, which exit would be the best, and where the Underground was situated. She smiled, popping her eyes open. The Doctor did the same. She tapped her head and winked, before standing up. She gave the Doctor another hug before turning towards Jake.

"I have to go back to my cell now," Donna stated, "I don't want the guards to get suspicious and hurt Jake." Jake blushed at her concern, before turning out of the cell. "Bye Doctor." The Doctor waved his hand and Donna quickly headed back over to her cell. He knew they could of tried to escape at this point, but he wanted to get everyone out. The escape plan needed to be flawless. If they had tried now, he would've gotten Jake in trouble and probably ran blindly into a trap. He had a plan and he was going to stick to it. In a few days they were going to escape. He knew it.

* * *

**I hope you enjoyed this chapter. :) I will try to update tomorrow. Please review and tell me what you think. Thank you. :)**


	28. Chapter 27

**Hi! Thank you for the reviews. Sorry, I didn't update yesterday, but I got into this show called Taking Over the Asylum starring a 22 year old David Tennant as a manic-depressive. It was honestly wonderful. It was funny and dramatic. Overall it was worth watching it. :) So, here's the next chapter. I hope you enjoy. Please review!**

Chapter 27

"The alien has two hemispheres," stated Dr. Jane Morley, from the psych ward. She glanced at the brain scans she had done on subject 13. "the left and right hemispheres like humans have but it has a separate third lobe. This third lobe is at the base of its brain and what I have witnessed, the lobe basically controls all motor and body functions. I found out about this when I had subject 13 walk around for a while. The third lobe lit up because of the movement." Morley brushed her graying hair out of her face as she studied the computer monitor with the image of the subject 13's brain. "The brain, unlike a humans, is green in color and much larger. It can store and analyze more information because of this." Dr. Morley glanced over at the Time Lord seated on a metal chair. Electrodes were connected to its head which sent information to the computer monitor that Dr. Morley stood next to. Its eyes were closed and it had a peaceful look on its face. If people noticed the alien, they would have assumed it was sleeping. But the colors and movement of its brain waves proved otherwise. On the monitor, the alien's brain showed quite a bit of activity as its frontal lobe lit up. The computer had given a 3D version of the brain including color and brain wave activity.

Dr. Black sat on a stool a few feet away from subject 13, notepad in hand. She wanted to gain as much information as she could about her test subject and volunteered to accompany it to the psych ward. She had watched Dr. Morley perform the first test, basic motor functions. Just from that they had learned quite a bit about the alien's brain. Dr. Black quirked her brows and pushed her glasses up her nose. "So basically subject 13's tertiary lobe controls all body and motor functions which basically frees the rest of the brain for intellectual pursuits," Dr. Black inquired, "Am I correct?"

Dr. Morley glanced over at the younger woman and nodded her head. "Precisely. Which means you're going to have to keep an eye on this one," Dr. Morley stated. She strode over to the alien, placing her hand on its cheek. Its freckles stood out against its pale skin. "Its a lot smarter than it likes people to believe. Look at its brain waves for God's sake. The brain hasn't even slowed down since our first test." Dr. Black glanced over at the monitor, before jotting down more notes. Dr. Morley bent down to the alien's level. It was restrained to a chair, sitting straight up. She brushed its hair back, staring in awe. "Full of wonders aren't you," she muttered, before clearing her voice, "Subject 13 open your eyes. I know you're not asleep. You're brain activity is too high for slumber." One brown eye popped open before the second followed. It glanced around the room, before its eyes landed on Dr. Morley.

"I know," it responded, "I was just thinking and resting my eyes." Dr. Morley rose to her feet, ignoring the alien's response. Its eyes following her movements curiously. "Dr. Black, you performed some test on subject 13's senses. Am I correct?" Dr Black glanced up at Morley from her note taking. Her eyes quickly ping-ponged between the alien and Morley, before she cleared her throat and took a professional tone.

"That is correct," she responded, she glanced at Morley indifferently, "Would you like to here some of our findings?" Dr. Morley nodded her head, zooming in on the image of the brain and quickly typing in some information.

"That would be wonderful," she stated, "I wish I was informed about the tests earlier. I would've happily taken some notes for future references. Can you tell me about your findings for the vision test?"

Dr. Black quickly flipped through her notes, to the day of the test, before clearing her throat. "We had stuck contacts into subject 13's eyes that allowed us to see what it saw. The contacts also allowed us a full analysis of its eyeball. So, what we discovered through the test... its eyes, unlike a humans which has rods and cones, are equipped with octagons which gives it incredible night vision." Dr Morley nodded her head, typing in the information. Dr. Black flipped a page in her notebook. "It can shift its vision outside the normal visual spectrum allowing it to see a total of 170 different levels of the electromagnetic spectrums. Which is absolutely incredible. It can also resist intense photo-emissions that would normally blind a human." Dr. Black flipped a couple more pages, before turning her gaze back over to Dr. Morley. She closed her notebook. Dr. Morley finished typing in the information, before turning back to Dr. Black.

"Anymore information you would like to share about its senses," she asked. Her eyes bounced over to the Time Lord who sat quietly in the seat. It apparently wasn't feeling very chatty at the moment. Dr. Morley had heard stories about the way the creature talked,fast-paced and non-stop. They had also told her it had a difficult time focusing on one thing at a time. It was easily distracted. Dr. Morley wondered if that behavior was normal for its species or if it was some form of ADHD. The alien's eyes seemed to dart around the room, focusing on one item for awhile before jumping to the next as a noise caught its attention. She had witnessed, when it first arrived to her lab, its extreme hyperactivity. It bounced all over the room, observing the different equipment, and speaking rapidly about everything. The guards were finally able to restrain it, before they explained to her that this was the most active it had been in a while. Its few days of rest probably helped its manic energy.

"This is from my own observations," Dr. Black continued, "When I had dealt with subject 13 on my own. Its eyes seems to change colors depending on its mood. So far I've only seen the normal brown and gold."

"Gold?" Dr Morley asked. Her eyebrow quirked in curiosity. She glanced back towards the alien, expecting its eyes to change color. It was looking at the far wall intensely before its eyes snapped over to Morley's. Its orbs seemed to bury into her soul, sensing everything she thought and knowing everything she was about to do before she did it.

"Uh huh," Dr. Black responded, her lips thin against her pale complexion. The woman honestly never smiled. "Its eyes turn a bright gold when it's angry or frustrated about something before that emotion dissipates. I have also noticed its brown eyes grow lighter when happy or excited or darker when it's in pain or depressed. It's quite incredible how expressive it is, considering subject 13's not human." Dr. Morley smirked slightly at the alien's annoyed scoff. It apparently was very opinionated as well. The Underground had definitely captured a hand full and she wouldn't be surprised if it attempted escape. From what she observed of its personality, It liked to play innocent and dumb before it completely exposed its brilliance. "You better keep an eye on this one," she muttered. Dr. Black glanced up.

"What," she asked. Dr. Morley rolled her eyes, turning to face Dr. Black.

"I said you better keep an eye on this one," she repeated, "It might try to escape." Dr. Morley noticed, from the corner of her eye, the flash of worry that crossed subject 13's eyes before it disappeared behind a mask of innocents. She smirked. She was definitely on to it.

Dr. Black scoffed arrogantly. "Escape!? Don't be ridiculous," she replied, "It's an alien. It doesn't have the brain capacity or motivation to figure out how to escape. Its been here for almost two months. If it wanted to escape, it would've by now." Dr. Morley rolled her eyes at the arrogance, smirking slightly.

"Suit yourself," she responded. She glanced back over at the alien, who watched her suspiciously. She wouldn't bring it up again. She was going to let the creature attempt its escape, so she could prove the Underground wrong about their assumptions of the aliens. Plus, when they recapture subject 13 it would be punished for running away and hopefully would learn not to try again. "Well," she stated, changing the subject. "I think its time to start the next experiment. I want to test its short-term memory. See how much it recalls when I flash a picture at it or give it a list of words. It would have to tell me the order of the list from first to last. I also want it to draw me a picture so I can see how its right hemisphere works differently from a humans." She started setting up her computer and the simulations she was going to use. "Ooo, I'll also give it some problems to solve, making each problem more difficult then the next so I can get a better idea of the structure of its intellect. Overall, today will be pretty mild on subject 13. I'm not going to punish it if subject 13 gets something wrong because I want to see how subject 13's brain processes information and comes to a conclusion or picks out the right choice." Dr. Black nodded. Morley heard the alien's sigh of relief, it obviously was preparing for the worst.

She marched over to subject 13's side, unhooking it from the chair. It rubbed at its wrist and reached for one of the electrodes before she slapped its hand away. "No," she stated calmly, "Those stay on. Come along." She walked over to a small table with a chair. The alien sauntered after her, still glancing around and touching items. She pulled out the chair at the desk and subject 13 sat in it. She bent down, putting restraints around its legs and connecting the chain to the table. She didn't want it wandering or jumping about. It quirked an eyebrow, before shrugging and facing the screen.

"Do you remember what I just said," she asked. The alien nodded its head, waiting for the first picture to flash. "Good." She stepped over to the computer and switched on the simulation. Each picture would stay onscreen for two seconds before disappearing. "Begin," she ordered. She showed the first picture.

* * *

The Doctor crinkled his eyebrows as he recalled the picture of the house and everything that was around the house. "The house was two stories, painted a robin-egg blue, it had four windows in front and red door with a little path. The curtains were white and the roof brown. There was a little dog sitting out front and an apple tree? Yes, an apple tree," he glanced over at Morley, who put the picture back on the screen. The only thing he forgot was the car driving up the street. He frowned when he spotted the car the second time.

"Good," Dr Morley stated. Before turning to the new picture. "Only missed one. A lot better than most humans did when I performed this test with them. They even had a longer period of time to observe the picture." The new picture flashed on and off quickly and the Doctor squinted, trying to remember everything.

"Um...A bear? Yes, a bear that had brown fur. Its leg was injured because I remember seeing red. It was in the mountains, holding a fish in its mouth...salmon." The Doctor tilted his head to the side, the picture had a lot more going on then the last one. He did have a photographic memory, but like all things it wasn't perfect. "Um...there was a pine tree next to it and it was standing next to a river. That's why it had a salmon in its mouth." The Doctor's eyes darted over to Dr. Morley, who was observing his reactions. Dr. Black sat to the right side of him, taking notes as usual. She didn't even seem to be paying close attention to the test at hand. The picture flashed back on, showing the exact photo the Doctor described. He smiled broadly.

"Excellent subject 13," she stated, "I think we should begin the list. In this test, I will show you a list of twenty words. You must tell me every word you saw on that list. You won't be punished if you miss some. I just want to see how much you remember. Ok?" The Doctor nodded his head leaning his head back, bored. This was too easy. Dr. Morley noticed his eyes straying away. "Subject 13 pay attention," she quickly commanded.

The first list popped up for a few seconds before it disappeared. "Tell me everything you saw in that order." The Doctor opened his mouth to respond.

* * *

"Its Memory is incredible,"Dr. Morley stated, "It recalled everyone of those words on those lists in the exact order. When I mixed it up, adding some numbers or words in different languages. It was still able to tell me." Dr. Black watched Dr. Morley. Morley was talking exuberantly, while at the same time trying not to distract subject 13 from its drawing. Dr. Black shrugged, biting at the end of her pen.

"I know I was there,"She responded icily. She didn't have the same exuberance that Morley had but she still respect the woman as an excellent psychologist. Morley's eyes drifted over to the hunched over alien. its eyes were extremely focused on the picture it was creating.

Morley had given it the task of drawing its own version of a pig. She gave it a bunch of different colored crayons and a sheet of paper and sent subject 13 to work. Her eyes darted over to the screen that was showing the 3D version of its brain. Its right hemisphere was lit up as it used its creativity and the left was providing it with a more realistic idea of a pig. its frontal lobe was completely active, morphing and moving as it drew. Dr. Morley stood up and made her way over to the Time Lord. She sat next to it, watching it draw. It was rather creative and obviously a talented artist.

* * *

The Doctor glanced up as Morley sat next to him, before returning his gaze back to the picture. He was actually enjoying this test. It was relaxing, compared to the others he was put through. He smiled happily to himself as he colored the pig purple and gave it big blue spots.

"Why's the pig purple," Morley asked curiously. The pig actually looked realistic except for the purple and blue spots. The Doctor glanced up, before shading in an area that needed to be shadowed. His tongue poked out, as he added in another shade of blue to the spots. "Pigs are normally pink, black, or brown."

"Its not an Earth pig,"he responded. Dr. Morley raised an eyebrow. The Doctor added something that looked like fuzz. Morley always thought pigs were only from Earth. Well, she learns something new everyday.

"What planet is the pig from then," she asked. She wanted to observe the Doctor's reactions to social conversations and get a reading into his personality.A sad, distant look appeared in his eyes. He halted his drawing, bowing his head slightly.

"My planet,"he whispered, eyes growing misty. He shrugged, continuing his drawing. Morley watched the reaction and frowned. _It must be homesick_, she reasoned. She watched him finish up the picture and handed it to her. She took it and placed the picture on the other side. "Ok, I think its time to test out your problem solving capabilities." She pulled out a large sheet of paper with equations on and a Rubik's cube, and a small book with problematic and moral scenarios. He took the items and set them down on his side of the table. He pulled out a pencil and begun filling out the equations quickly, barely even glancing at them. Dr. Morley's mouth dropped as he got each problem right without any hesitation.

* * *

The Doctor fiddled with the Rubik's cube as Dr. Morley read him another possible scenario. The Rubik's cube was almost complete. He just had a few more pieces to put in place.

"Ooo, here's a good one," Dr. Morley stated, "There was a war between your people and another." The Doctor glanced up from the Rubik's cube. The moral dilemma sounded familiar. "Your people wanted to win this war, but the only way they could was by destroying other civilizations that weren't apart of it. If they won many people would die but if they lost...they would die. It is your decision to decide who should live. Your people or the other civilizations. Please explain your reasoning." Morley glanced up, waiting for an answer.

The Doctor was frozen, his mouth gaping open. The Rubik's cube fell out of his hand and smacked the table. His eyes grew misty as tears prickled his eyes. His head drooped and his hands covered his face, he heaved deeply. "Subject 13. You must answer the question," Dr. Morley stated. She watched his reaction to the hypothetical scenario. It was one she asked every alien subject that walked through these doors. They always chose their home. Which was completely understandable. She would probably choose her home as well.

The Doctor sniffed and raised his head, clearing his throat. "Everyone deserves a chance to live," he responded, "If i-it m-meant that other people will die because of our war then we should die. There are children in those other civilizations who wouldn't know what the universe was like because we destroyed them before they had the chance. It was our own fault and we dragged other planets...I mean civilizations into this war that had no part in it. So, I choose save the other civilizations." The Doctor laid his head on the table and fiddled with the Rubik's cube once more. Morley watched curiously, she had never received a response like that before. This was a first. She sighed and rubbed at her eyes as the Time Lord finished the cube.

"Ok, We're done for today," she packed up the book and grabbed the Rubik's cube that the Time Lord handed her. She walked over to the Doctor's side and removed the electrodes, before quickly unhooking the restraints.

The Doctor stood up and stretched his muscles, as two guards and Dr. Black approached him. The guards grabbed his shoulders and forced him out the door.

"To the training room," he said soberly. The last question had really struck too close to home and it hurt. He marched out of the room, preparing himself for a long, strenuous training session.

* * *

**I hope you enjoyed this chapter. There will be a couple more before the escape attempt. I'm glad you're enjoying the story and please review and let me know what you thought. Thank you! :)**


	29. Chapter 28

**Hi, Thank you for all the reviews! :)There is some swearing in this chapter. Nothing to bad though. So, Yeah, here's the next chapter. Please review! I love reviews.:)**

Chapter 28

Whizzzz...The Knife flew through the air, hitting the mannequin target perfectly in the chest. Another Knife impaled the Mannequin's eye, and the third hit the Mannequin's thigh. The Doctor picked up a fourth knife and flipped it in the air. He caught the handle and quickly chucked the sharp blade, barely measuring out the target. The Knife whizzed thorough the air, impaling the mannequin's shoulder. The Doctor stared impassively at the Mannequin's shredded remains. Each knife struck perfectly in the middle of the target.

The Doctor's ears twitched as he heard the slow clap of Major Johnson. He turned his head, ruffling his brown hair back. Major Johnson marched forward still clapping, his smile cold and cruel. "Excellent, Subject 13. Not one miss," The Major congratulated, "I think you'll make an excellent asset to our alpha team. I believe we can send you on your first mission pretty soon." The Major strode over to the Mannequin, his fingers stroking the knives. The Doctor warily watched, preparing himself to dodge any flying blades.

The Major sometimes enjoyed doing surprise attacks, keeping the Doctor on his toes. It had happened once. The Doctor had finished a practice round with the weapons that the Major had chosen for him. The Major had congratulated him on a job well done, before quickly turning and throwing the sharp blade at him. The Doctor didn't expect it and ended up having a knife stuck in his leg for twenty minutes before a medic team made their way over. During that time, he received a lecture, about how he needed to pay attention or next time the strike might kill, as he bled out on the floor. Not one of his most satisfying days that's for sure.

The Major's fingered the handle of the knife, before sliding his fingers down the cut the knife made in the mannequin. "All we need to do is get you comfortable with killing. I think the problem is you've killed from a far distance, but up close is a little too personal for your liking. I don't believe you'll have a problem after your first." The Major took a quick glance over at the Doctor, before he slowly walked around the mannequin. "You surely have the skills." The tip of the knife had popped out at the other end of the chest.

The Doctor glared at the Major, his jaw set stubbornly. "I will not kill anyone for you," The Doctor stated. He gritted his teeth in frustration, eyes never lingering far from the Major. His muscles tensed expecting a blow that never came. Instead a low, dark chuckle came from behind the Mannequin as the Major stepped into view.

"I don't believe you have a choice in the matter," the Major responded icily. He strode back in front of the mannequin, his hands behind his back. "The sooner you learn that you're Underground property, the easier your life will be." The Major quirked an eyebrow. "I believe we have had this conversation before. Don't you?" The Doctor glared, steadily watching the Major's hands. The Major turned away, his fingers curling around a handle. He yanked it viciously out of the Mannequin's chest and threw it. The Knife spun quickly towards the Doctor. He twisted out of the way, the knife hitting the punching bag that was once behind him. Sand spilled out of the bag. The Doctor quickly glanced over at the punching bag, before turning back to the Major. The Major had a sickly sweet smile on his face. "Very good."

The Doctor's stance was still tense, expecting another attack. The Major rolled his eyes, arms crossed. "I won't be attacking again, our day is far too busy for that. Come along Subject 13, we're heading to another training room. I'll explain when we're there." The Major turned on his heels, he glanced over at the guards that stood along the walls, all holding tranquilizers or tasers. The walls were also holding hidden guns in case the Doctor tried to escape or attack the humans. It was all safety precautions, until the scientists had finished building the device that would dampen the Doctor's abilities and provide them with easier control access over the Time Lord. The device wouldn't be sent to him for another few days. "Clean up this mess," the Major ordered the guards in the room. His had gestured to the knives and mannequin. "And when you're finished, bring the knives to me. Subject 13 will be using them at the end of this lesson." The guards nodded their heads, responding with a quick 'yes sir.' The Major turned to the Doctor. "Come along, subject 13." The Doctor quickly followed the Major.

* * *

The Doctor stepped into a large, white room with glass window panels along one side. People were looking through the windows and sitting at chairs drinking coffee. One man had earphones on and a microphone in front of him. People paced along the windows. The Doctor felt like he was on display. Like he was some wild exotic animal that no one had ever seen before. The Major stepped through the doors, marching over to the Doctor. The Doctor's brown eyes darted around the room, landing on a dark red smudge on the wall across from him. He gulped, his brain quickly piecing the clues together and deciding on a conclusion. It was a death arena. The type of arena that the Romans would watch two gladiators fight until one died. Except this arena was not outside, but in a highly secretive agency, that turned aliens into assassins. The Doctor's face burned a bright red, anger and frustration highlighting his features. His teeth gritted.

He turned to face the Major. "A death arena? You want me to kill some innocent being for your own entertainment. I won't participate." The Doctor crossed his arms stubbornly. The Major snarled, grabbing his arm, and pulling him close. The Doctor stiffened as hot breath brushed his ear.

"You will participate," the Major hissed, "You have no choice. You won't kill on your own, so now I have to force you. If you continue to disobey my orders, I will find something else that will persuade you to kill because threats of punishment doesn't seem to have any affects on you. The alien is not innocent. Far from it and it will kill you if its given the chance. Understood?" He yanked the Doctor's arm once more and the Doctor steadily nodded his head. He glared at the Major, his stare penetrating Johnson's. The Major released the Doctor's arm and ruffled his hair, like an owner would a dog. "I don't want you dead. You're far more valuable then the piece of shit that you'll be fighting."

The Doctor smirked slightly, rubbing his wrist. "Glad I've grown on you." The Doctor gave a cheeky grin. The Major sneered, turning away. He walked back through the doors, his face appearing on the other side of the window. The Doctor eyes shifted to the far wall of the room where a large door was situated. The Doctor turned his gaze back to the windows. Colonel Graham now stood next to the Major, his arms crossed behind his back and black sunglasses on his face. His jaw was set tensely, awaiting the fight as more scientists and guards lingered in later. The Doctor turned back to the door on the other side.

"Great," he muttered, "An audience." He felt the vibration of heavy foot-steps roll along the pristine white floor. The Doctor quickly got into a fighting stance. He was first going to try and talk to the alien, strike a deal, and protest against this treatment. But if things got out of hand, he wanted to be able to run and dodge each blow. It wouldn't help him if he got knocked out and ripped to shreds.

The doors slowly glided open and a large alien stalked out of the dark. The creature was at least seven inches taller than the Doctor and built like a tank. All muscles and no fat. he sported a green Mohawk that ran down his head and red pupils with black irises. his skin was a whitish-gray color and long, sharp teeth covered his lips. The aliens tongue was split into two, flicking out like a snake. In his hand was a weapon that looked like a mix between a bat and an ax. He wielded it threateningly and began slowly stalking over to the Doctor. His veins straining against his neck.

The Doctor put on the friendliest smile he could muster and he waved his hand. "Hello,"he chirped, "I'm the Doctor." The Doctor glanced at the aliens sharp teeth. "Nice teeth." The alien growled, swinging the sharp weapon at the Doctor's head. The Doctor rolled out the way, walking backwards as the second swing almost took off his head. The Doctor glared.

"OI! That's not very nice," he exclaimed, "I've been nothing but charming and you tried to remove my head." The Doctor crossed his arms indignantly. "And they call me rude,"he sniffed. The alien swung the weapon around once more, the Doctor duck before twirling out of the way. The alien growled in frustration, his eyes bulging from the sockets. "Hey, Calm down," the Doctor reasoned, "I just want to be your friend. I don't want to fight you. We don't have to listen to these humans. We can sit back, enjoy the scenery..." the Doctor glanced around the blank room, before turning his gaze back to the bloodthirsty alien. "Well not much enjoying the scenery anyways, but none the less we can have a good chat. Exchange stories and secrets and sleep under the artificial lights." The Doctor smiled broadly, taking another step back. "How does that sound?" He was answered by another swing of the bat that slammed into his guts. The Doctor grunted, stumbling. "Ok," he gasped out, "No stories. But really. Do you honestly want to kill me?"

"Yes," the creature hissed, his tongue flickering out of his mouth, "I want your blood spread across the walls and your guts dangling from the ceiling." The creature swung the bat again but this time the Doctor was ready, he grabbed the bat and yanked it out of the aliens hands. The alien stumbled forward from the force, snarling angrily. The Doctor tossed the weapon to the side.

"Lovely," the Doctor stated, "I was hoping we could come to an agreement, but apparently you're to daft to figure that out." The alien growled at the insult and ran forward, the Doctor quickly spun out of the way. The punch whizzing past his ear. "Maybe I'll need to enunciate better or simplify my words to that of a caveman's."

The alien snarled and quickly jumped forward, wrapping its long,skinny fingers around the Doctor's neck and lifting him off the ground. The alien screamed and spittle splattered the Doctor's pale face. The Doctor kicked out as he felt the air squeeze out of his lungs and his respiratory bypass system switch on. "Y-you're m-making a m-mistake," The Doctor choked out, his eyes bulged out of his sockets. "I d-don't g-give s-second ch-chances." The alien chuckled and squeezed harder, the Doctor's quickly scrambled for the aliens fingers, trying to peel the long fingers off his throat. The aliens fingernails dug into the Doctor's soft skin.

"I don't give any chances," the alien hissed, digging his nails further into the skin. Blood ran down the Doctor's neck as he kicked out.

* * *

"Damn," The Major barked, banging his fist on the console, "Stupid stubborn alien!" The Major kicked out at one of the chairs, a hand brushing his blond hair back. The guards and scientists watched the reaction, before their gaze turned back to the window, watching the fight. _Bang_. Subject 13 hit the glass window hard, before sliding down it and leaving a slobbery trail. They saw the larger alien race forward, grabbing subject 13's hair, and tossing it across the room. Subject 13's body tumbling violently across the floor.

Colonel Graham turned to Johnson. "I thought you said Subject 13 was a trained fighter," he growled. His hand gestured to the brawl out in the arena as the Time Lord was tossed against another wall. "This is not a trained fighter." Johnson's face burned with humiliation and anger. He was going to punish the freak if it survived.

"It is," Johnson coldly stated, "It's just trying to spite me because I told subject 13 it had to kill. You don't understand how stubborn that animal is."

"I do," the Colonel responded. His neck stretched and arms crossed in front of him. "That's why I intrusted you with its training. Find another way to make it behave." Johnson ran a hand through his hair, his face burning with contempt and fury. He wanted to kill the skinny freak. Burn it alive. Bury it. Anything to make it suffer. But it doesn't care about its own pain. A light bulb flashed over Johnson's head and a cruel smile curved his lips. But it doesn't like seeing others in danger or hurt. Especially a certain ginger. Johnson turned to the guards.

"Get the ginger from the cells and bring her here," Johnson ordered, "I think its time subject 8 had a new toy." The guards saluted, before turning out of the room.

A smirk curved the Colonel's lips. "Good thinking Major," he complimented. The Major smiled at the compliment. The yells and curses echoed down the hall as the ginger woman was dragged into the room by two brutish guards.

* * *

The Doctor was slammed aggressively against the floor. He crinkled his nose, groaning slightly before he was flipped over onto his back and a large foot crushed his chest. The monster...because that was the only description the Doctor could think of right now...chuckled darkly as drool slid from between its lips, splashing the Doctor in the face. The Doctor sighed, concluding that this wasn't one of his most brighter ideas. He probably should of done a bit more fighting and attempted to at least knock the beast out.

"I had my fun," the beast growled, "Now its time for the death blow." The alien lifted its arm and was about to strike, but the Doctor wriggled out from under the giant foot and rolled out of the way as the giant hand slammed into the ground. The monster howled in pain as its hand cracked from the force. The Doctor quickly jumped to his feet, skidding on the blood that covered the floors. He ran a hand over his bloody nose, coughing. He stood at ready, waiting for the alien to attack. A loud crinkling echoed in the room.

"Subject 8 you have a new target," the man said over the intercom. The intercom shut down and a familiar shout was heard as the doors slid open.

"Let go of me you bastards," Donna shouted,"Or you're going to pay for this." The two men laughed at her struggles and shouting. They tossed her unceremoniously into the room before slamming the door shut. The strong smell of blood wafted Donna's nose. She turned to see a giant, ugly alien stalking towards her. Donna backed away. She could hear the Doctor's shouts of protest from a distance, but all she could really think about was the giant monster.

"Yummm..." the creature hissed, "Fresh meat." It launched at her and Donna shrieked in surprises, stumbling out of the way. She took steady steps backwards until her back hit the wall. The Monster moved closer, lifting its hand.

"Y-you really don't want to eat me," Donna squeaked out, "I d-don't taste very good. I think you would be happier with a mars-bar or something. PRINGLES! Yeah, I think you would really like pringles. All the different flavors. You could have a full course meal." The Monster drooled and Donna face crinkled in disgust. "Ewww...Watch where you're drooling, sunshine." The Monster stepped intimidatingly closer.

"Who said anything about eating you," the monster growled, "I just want to kill you." It raised its hand about to strike, but a blur struck it in the side and Donna gaped as she spotted the Doctor landing steadily over the fallen monster.

"Oi, leave the lady alone," the Doctor shouted, "Your fight is with me." The monster growled and got to its feet, moving closer to the Doctor. It's split tongue running lazily over its teeth. It swiped at the Doctor but he dodged the large hand. The Doctor kicked the monster in the side. "I told you I don't do second chances." The Monster growled and the Doctor jumped forward, twisting its arm.

Donna watched in awe as her skinny-martian fought off the monster to protect her. His movements were fluid and precise. Each punch was aimed for a pain center and each kick was used to trip it up. He spun and danced out of the way of each swing, flipping over the monsters head when it grew to close. Donna frowned and stood up. What was she doing behaving like a damsel in distress? She had boyfriends a lot uglier than that thing. Donna stood up and quietly walked around the fight. At the moment, the Doctor was on top of the aliens back, pulling at its green hair and punching it in the face before the monster grabbed the Doctor's shirt and flung him off its back. The Doctor skidded across the ground, jumping back to his feet and leaping, kicking the monster in the face with a bone-crushing kick. He spun to the ground, landing silently on his feet, like a cat.

Donna picked up the large bat-ax weapon and slowly tip-toed over to the monster. The monsters back was facing her as it viciously fought the springy Time-Lord. The Doctor quickly bent backwards at one of the strikes, before jumping up and swinging his foot into the monsters solar plexus. The monster bent over and Donna swung the weapon at the monsters head. A loud bang was heard and the monster growled in anger and pain, clutching its head. Its head quickly swiveled around to face Donna. Donna waved the the bat-ax hybrid thing around threateningly.

"Do you want anymore of that, sunshine," Donna shouted, "Because I have a whole lot more where that came from." She held up the bat, like a batter in baseball. The Monster growled, quickly grabbing at Donna. But the Doctor tackled the alien, grabbing its legs, and putting forth his full strength into knocking it over. The monster fell heavily and the Doctor did a rapid spree of punches and kicks, trying to keep the alien down. The alien shot out a hand, wrapping its fingers around the Doctor's shirt collar, and yanked him down. The Doctor slammed into the floor, quickly kicking the monster in the teeth, and escaping its grip. Donna shouted, swinging the weapon.

"Let him go ugly!" She was about to swing the bat but the Doctor grabbed it, breathing heavily. Sweat and blood glistened off his face as perspiration ran down the tip of his nose. "It's over," he muttered, "It's unconscious." Donna dropped the bat, nodding her head, Adrenaline still racing through her veins. She threw her arms around the Doctor's neck, not even noticing the sticky sweat and blood that covered his body or the people who were watching them. She had never been more scared in her life. The Doctor's hand repetitively rubbed her back and he whispered comforting words into her ear.

They heard a loud beep and the swooshing of doors opening. They quickly pulled away, stepping apart. The Major stiffly and coldly marched over. His gaze never leaving the Doctor's. The Major cautiously stepped over the pools of blood, which was stupid considering that the once white floor now had a pinkish tint. The Major glanced over at the alien, lying on the ground unconscious before turning his cold gaze back on the Time Lord. He kicked the unconscious alien in the side, reddish blood oozing from the alien's wounds.

"Is it dead, subject 13," the Major asked, he crossed his arms. The Doctor shook his head, watching the Major steadily. The Major growled in anger, before his gaze stopped on Donna.

"I told you, Major, I won't kill another being in cold blood," The Doctor stated.

"We'll see about that," The Major sneered. He quickly grabbed Donna's arm and yanked her forward. Donna stumbled into Johnson's chest from the force of the pull, before being flipped around and forced to face the Doctor. A gun was placed next to her temple. She struggled slightly until she heard the guns trigger click as the safety snapped off. She was pulled backwards, listening to the Doctor shouting at the Major to leave her alone. She saw the Doctor run forward before halting as guns were leveled at him. He slowly put his hands up and Donna was tossed to the ground. The guards stood in a protective semi-circle around the Major and Donna, ready to shoot the Time Lord dead if he tried to come any closer.

The Major flicked his hair back as sweat dotted his top lip, he pulled out a cattle prod."Subject 13, I want you to kill that alien or your little friend here will be tortured and afterwords killed." Donna felt tears prickle her eyes as she watched the Doctor hesitate. She cleared her voice.

"D-Doctor d-don't k-kill. This is above you," She shouted out, "I won't allow you to sell your morals to these scums of the Earth. Please..." She was smacked in the back as electricity shot through her body. Her eyes bulged as a thousand prickly needles ran along her skin. A strangled cry released from her throat. The Doctor screamed at them to stop.

"Kill the alien or your friend will die," the Major repeated, "I want you to break its neck." The Major twisted his fingers through Donna's red hair and she let out a pain-filled shriek. The Doctor nodded his head.

"Ok," he cried out, "I'll do it. Please just stop hurting her." The Doctor slowly walked over to the alien, he bent down and wrapped his long fingers around the neck. "I am so sorry," he stated. He twisted the muscular neck hard. _Crack!_ The neck snapped, dangling to the side. The eyes of the alien opened for a second before glazing over and turning deathly empty. The Doctor felt his bottom lip tremble. He didn't know the alien before it was turned into a monster but he knew it was a victim just like him. He probably had a family out there wondering where he was. Now he would never return home. The Doctor felt a strangled cry leave his lips, tears glistening in his eyes. More blood on his hands. Why was he stained with so much blood?

He turned a tired and broken gaze over to Donna. Tears dripped down her cheeks. He sighed. She would never be able to look at him in the same light again. He was a monster. A murderous killing machine and he deserved no better then this place. His eyes drifted over towards Donna, tears still streaming down her face. He scared her. The Doctor's eyes drooped and he banged his fist angrily against the floor. A monster. He felt every part of him freeze over. His hearts going cold. He glanced over at the now dead alien. He was no better than that creature on the ground. He rubbed at his blood stained hands desperately trying to remove the stains. So many people, just another to add to the ongoing list. He gritted his teeth. The Major was going to die. He slowly stood up, his head tilted to the side. Donna was no longer in the room, instead behind the glass window. The Major was the only one left, except for a few guards making there way over to the body.

"String it up against the wall," The Major ordered the guards. "I want subject 13 to finish off the day with target practice before it's sent back to its cell!" The knives were next to the Major's feet. All it took was a quick slash to his throat and the Major would die. Humans were oh so delicate. He felt a vicious smile twitch at his lip and manic laughter bubbled from his lips. All it would take was one slash to kill the man who made him a cold-blooded murderer. One slash and the Major would drop dead. Or maybe he'd prefer the bastard to bleed out. Suffer for all the pain he put the Doctor through.

Quicker than the eye could blink, the Doctor threw himself against the Major, pulling out a knife and resting it against the soft human flesh. The Major leaned against the glass window, his adam's apple bobbing. The guards shouted around him, grabbing their guns. The Doctor slowly dug the knife into the Major's throat.

"This is what you made me into,"he hissed, "A murderer and because of that I'm going to kill you." He heard the guns cock, all aiming at his back. He laughed manically at the scenario. The laugh was more hysterical then actual glee.

"Do it then," The Major dared. His cold eyes never leaving the mad brown eyes of the Doctor. He smirked. "Like I said you're just an animal." The Doctor felt his hand shake and the knife loosened in his grips. He heard buzzing as the intercom switched on.

"Doctor please," he heard Donna's voice beg, "Control yourself. You're far better then this scumbag. Please Spaceman, Don't make me loose hope." The Doctor glanced up, spotting Donna on the other side of the glass panel. Men were trying to pull her away from the microphone as she struggled and kicked out, screaming in rage. The Doctor dropped the knife and the Major took the opportunity to restrain him. He slammed the Doctor against the glass, holding him still. The Doctor watched as the guards dragged Donna out of the room. The Major pulled the Doctor away from the window and threw him to the ground. The Doctor felt the rage die as despair enveloped his soul. The Major bent down, all guns pointed straight at the Doctor.

"I knew you couldn't kill me," the Major mocked. "too weak." The Doctor dazedly stared at the bloody ground. The Major pulled him up and pushed him towards the body that hung from chains. "Target practice," the Major stated, "I want you too do exactly as you did early today with the mannequin." The Major handed the Doctor the knives, all the guns pointing at him. His fingers wrapped around the handle of the first knife, tears sliding down his face as he looked at the hanging body, blood puddling underneath.

"I'm so sorry," the Doctor whispered again. He pulled back his arms, lips wobbling with suppressed emotions. He threw the knife. The blade landing in the dead alien's chest with a soft squelch.

* * *

**Hi, thanks for reading. This chapter was definitely high-packed in action and angst. I don't know if the Doctor seemed a little ooc or not, but if he did I wanted that. The Doctor is changing emotionally and morally and killing the alien was sort of on the edge of tipping over to the dark side. Except he is still fighting against it all. That is why he didn't kill the major. He feels like a monster but he's not quite there to completely kill in cold blood. Yeah lots of emotions. Plus, I'm sure some of you are wondering why the Major gave the Doctor back the knives after he was almost killed. Well, he's an arrogant bastard who believes that he has complete control over the Doctor. He just doesn't realize that the Doctor is still fighting to protect and save his morality that's why his life was spared. Also, if you guys noticed the alien was either described as he or it. I did that on purpose. I wanted to show the Doctor at first thought of the alien as a person before the alien showed he was a monster. By the end the Doctor called the alien a he as the Doctor thought about the alien's family out there, showing that the Doctor excepted the alien as a person once more. So, yeah hope you enjoyed this extremely angsty and emotional chapter. Please review and tell me what you think. I know it was a shocker to have the Doctor actually kill. Please review. **

**PS: Some people are concerned that the Doctor is going to bow down and bend to the will of these humans. Don't worry that won't happen. I would never allow that. Like many people have said in their reviews the Underground just doesn't know who their dealing with yet. :)**


	30. Chapter 29

**Hi, Thank you for the reviews. :) I know some people are worried about the Doctor bowing down to these people but I would never allow that. The Doctor doesn't bow down to anyone. He is definitely too strong for that. He's just going through some tough times. :) I hope you continue reading and please review and let me know what you think of the next chapter. :)**

Chapter 29

"Donna, I'm sorry you had to witness that," the Doctor stated soberly. He rested his head against the wall, exhausted. He was not proud about what he did, but if he didn't Donna would've been hurt or worse. He would rather die then allow that to happen. So, he did exactly what the scums of the Earth asked and he felt terrible about it. He knew he wasn't helpless or weak, look at everything he was dealing with. The Major was trying to get under his skin which almost worked. The Major would've been dead earlier that day if it wasn't for a certain ginger begging him to stop. The Major and everyone else here doesn't know who they are dealing with and the Doctor wanted to keep it that way. It made it easier to put together his escape plan if they believed he was just a know-it-all talkative idiot. He was not proud about killing the alien, but the options were either the alien or Donna and he couldn't bare the thought of losing Donna.

"It's fine Doctor," she responded solemnly, "I'm not judging you. You did what you believed was right. I'm glad you chose me because I really didn't like the idea of dying. I was just worried about how you would feel. I didn't want you to have anymore blood on your hands." The Doctor gazed over in Donna's direction, smiling softly.

"Donna I'm always going to have blood on my hands," the Doctor answered back, "From the war and other events that I have been forced to deal with. This is just one more." Donna nodded her head.

"I was scared,"Donna revealed, "When I saw your eyes turn that dark shade of brown. I thought you loss it. I was scared if you killed the Major, you wouldn't come back and that thought frightened me. I was terrified that you would turn towards that darkness you were telling me about. I didn't want that to happen to you."

The Doctor rubbed his eyes, sighing heavily. "Don't worry about it. I stopped myself. I'm fine Donna." Donna nodded her head, wrapping her arms around her stomach. She glanced over at the Doctor, noticing his eyes were glazed and unfocused.

"Doctor what's wrong," she concernedly asked. The Doctor snapped out of his trance and shook his head. He brushed a hand through his hair.

"I spotted Colonel Graham earlier today," the Doctor replied. He jumped up and begun pacing his cell, hands clasped behind his back, and eyebrows knitted. "You're right something is wrong with him."

Donna perked up. "So he's an alien or something."

The Doctor shook his head,tapping his fingers against his mouth. "Or something. He's definitely human. I'm pretty sure of that, but something just isn't right about him."

Donna stood up and strode over to the front of her cell. She watched the Doctor's rapid movements. "Doctor if he's human then what's wrong with him. When I met him, he was talking about some event where the Earth moved. I'm pretty sure our future selves were there, but I guess all my records and documents disappeared after that. It was like I never existed." The Doctor spun around towards Donna, his eyes crazed as he tried to fit the pieces together. His hair stuck out in every direction.

"Anything else that caught your attention," the Doctor asked quickly, "Come on Donna I know you picked up more then that." Donna glared at his pushiness, crossing her arms. "Sorry," he stated.

"I was just about to tell you, Time-boy," Donna exclaimed. She sighed, leaning against the wall. "He was talking about how aliens murder families and how they have no emotions." The Doctor slowed his pacing, staring at Donna intently. She could practically hear his brain ticking with life. "The way he said it, I could hear the pain in his voice even though he was trying to cover it up with his cold demeanor."

The Doctor nodded his head. "Do you think..."

"Do I think that Colonel Graham lost his family during the event when the Earth moved. Yes. I think that's why he turned against aliens, finding something to blame for his lost. It's his way of getting revenge. One bad alien kills his family which dubs all aliens evil."

"My thoughts exactly," The Doctor agreed. He jumped up onto his bunk, before falling backwards, and leaning his head against the ground, feet sticking straight up in the air. "But the question is what is he planning?" The Doctor turned his head in Donna's direction. "We know he and the rest of this agency are experimenting on alien's and/or training them to be professional assassins. My bet they're trying to turn these aliens against their own kind."

"But that's already been obvious from the start," Donna retorted, "Why else were they creating living weapons unless they wanted to kill their enemies. Which in this case are the aliens."

"It's a very clever strategy. If you can't beat them send you're own brainwashed prisoners after them," the Doctor replied, "It keeps their hands cleaned and out of the battle. But what if brainwashed alien soldiers just wasn't enough. They still don't feel protected because these aliens still have the hate and desire to turn against their cruel captors."

"They believe that only 'trustworthy humans' can protect them,"Donna continued, "Why would they need aliens to protect them and do their dirty work when they could do it just as well."

"But not all the employees have heard about this plan," the Doctor stated, "only the leader of this organization. The others are in the dark and the Colonel doesn't want to reveal his private little experiment until the time comes."

"That's why they're still training the aliens. The Colonel hasn't revealed his plan yet..." Donna was interrupted by the light patter along white tiled floors. The Doctor did a backwards somersault, landing on his feet before leaning against the wall casually. Dr. Carter strode into the room, his wicked smile creeping across his face, his long labcoat brushing the ground. His black eyes met the Doctor's. The Doctor shrugged before sauntering up to the front of his cell. This was definitely a newer way of being dragged off to another lab. Normally guards were around. As if on cue, two burly guards appeared right beside Carter.

"Where am I going this time," he asked casually. Carter frowned, before his eyes focused on Donna.

"You're not going anywhere," Dr. Carter replied. He snapped his fingers and the two guards enter Donna's cell. They grabbed her arms and held her still as she thrashed around, shouting.

"Let go of me," she snarled. She gave Dr. Carter her version of the death glare, "If it isn't the weasel. Come to have a nice chat, creep?" Dr. Carter didn't answer instead pulling out a scalpel and a cup.

"Oi, leave her alone," The Doctor shouted, "Don't you dare hurt her." The Doctor banged his fist against the wall, face burning with anger.

Dr. Carter scratched the scalpel along Donna's skin scraping flesh off. Donna gritted her teeth as the knife ran down her arm, blood slowly dripped from the wound and Dr. Carter caught it in the cup before placing the piece of flesh in it as well. He screwed the cap on and put the cup and scalpel back into his pocket. "Why the hell did you cut me, you creep," Donna growled.

Dr. Carter smiled sinisterly, "You've been down here with the aliens for a long time and have been with subject 13 even longer. I just wanted to see if their DNA altered your own. If you're any less human then you were previously."

"That's the most ridiculous thing I have ever heard," the Doctor shouted, "I don't know what you're playing at Carter but I don't like it."

Carter ignored the Doctor's shouting,instead turning out of Donna's cell and marching back down the hall. The Guards released Donna and followed quickly behind. They marched past Bobby who had just arrived to do the daily cleaning and chat with the Doctor. Donna held her arm close, trying to halt the bleeding. The Doctor brushed his hand through his hair, irritated. They had to get out now...or at least Donna.

"Doctor," Bobby asked, "Is everything alright?" The Doctor glanced over at Donna before his eyes shot over to Bobby.

"We're escaping tonight," the Doctor stated, "the device is ready and it's time to get Donna and everyone else out of here." Bobby nodded his head. There was a collective gasp from the other aliens and immediately the cell block came alive with activity.

"Alright, I'll alert the others on my rounds," Bobby responded, "I'm going to miss you Doctor. Donna."

"Bobby I don't want you to be here any longer then you have too," the Doctor stated, "When the first alarm sounds, I want you to bolt and don't look back." Bobby nodded his head in understanding.

"I wonder why we haven't been stopped before," Donna questioned, "I'm sure they've heard our conversations through the surveillance cameras."

Bobby shrugged his shoulders. "The surveillance team is arrogant. I've gone into the surveillance room to clean up before and I noticed the group doesn't really pay attention to the footage. They keep the sound on mute. I think the cameras are mostly used for discouraging escapes."

The Doctor grinned. "Well, that's a point on our side. Bobby go alert the others and I'll see you later."

Bobby nodded his head, quickly cleaning up, and putting things away. He pushed his cart out through the door and headed off to alert the other aliens.

"Doctor what about the other aliens in the labs," Ama, the young Shian, asked, "They'll be left behind."

"I'll go find them while the rest of you escape this place," the Doctor responded, "No one's going to be left behind."

* * *

**I hope you enjoyed this chapter. Please review and tell me what you think. :)**


	31. Chapter 30

**Thank you for all the wonderful reviews. I hope you like this next chapter. Please review. I love reviews! **

Chapter 30

The Doctor popped an eye open as he laid on his bunk, his arms pillowing his head. He rolled off the hard slab, they called a bed, reaching under it. He pulled out the device. The device was long and thin, a little chunkier then his sonic screwdriver and had a satellite shaped disk for the head. He held the device, quickly cranking the lever on it and the disk began to spin, speeding up the faster it was cranked. Light flashed out of the satellite disk, as electricity began to spark. The Doctor clicked a button and the device brightened with light at the tip. The Doctor smiled widely, laughing.

"One sonic device coming up," he whispered to himself. He walked over to the forcefield, touching the lit piece to the electric forcefield. A loud rumbling sound was made, as the forcefield sparked and collapsed.

An alarm blared and all the occupants of the cell block woke up. The Doctor cranked the lever and blue energy shot out disabling the surveillance cameras. The Doctor stepped out of his cell and quickly typed in the disabling codes into the control pad next to his cell. If he could retype the codes he could use those codes to shut down all the cells in the cell block at once. His fingers moved quickly along the keypad before he jammed his device into the control panel. With a loud zing all the forcefields shut down and the occupants stepped out in shock. He heard silent cheers and clapping from the released prisoners. Donna raced over to him, throwing her arms around his neck. The Doctor hugged her back before pushing her away.

"No time for hugging and chatting," the Doctor stated, taking command of the situation immediately, "We need to get out and find the others. Everyone knows the plan correct?" The alien occupants nodded their heads. "Excellent." The Doctor turned to the alien shape-shifter, who could turn his body into a solid twelve-foot tall rock monster from a single thought."Roc. May I call you Roc." Roc nodded his head. "I need you to turn into your rock form."

Roc shook his head and pointed at the metal collar around his neck. "I can't." The Doctor nodded his head in understanding, before sticking the device against the collar and clicking the button. The collar fell off and Roc immediately begun changing form. Roc roared, his rock head flinging up. The Doctor made his rounds disabling each restraint the aliens had on. Donna raised a brow.

"You built a sonic screwdriver from scratch, didn't you?" She asked. The Doctor shrugged his shoulders giving a cheeky smile.

"I like to call it a sonic device," he retorted, "Alright everyone lets get going." Roc ran forwards first, he threw his full body weight against the door. The door crumbled from the powerful rock monster. Darts and bullets lightly tapped Roc's chest, falling to the ground crumpled and bent. Ama stepped out next covered by Roc's stone body. She immediately began telepathically searching the room for guards.

"Two groups are coming our way," she reported. Her eyes were slightly glazed over as she focused on diverting the guards. The Doctor and Donna ran out next. The Doctor used his device like radar as he scanned the walls, looking for wiring that was connected to the traps. A loud beep was made and the Doctor quickly cranked the lever. Blue energy shot out, melting the hollow wal,l and destroying the wiring. The patter of bullets, hitting Roc immediately seized. The rest of the aliens filed out into the room and the Doctor breathed heavily.

"Alright, Donna I want you to get this group out and find a warehouse or some type of safe haven that you can direct the aliens too. You know where the exit is. Ama will provide a psychic covering so no one spots your departure," The Doctor stated. Ama turned towards the Doctor, giving him a quick kiss on the cheek.

"Thank you," she stated, her lips wobbled with emotion.

"It's not over yet," He responded, "Go. Donna will get you out of here. I can already hear twenty pairs of feet approaching. They're growing closer."

"You're not coming are you," Donna stated knowingly.

The Doctor shook his head. "I need to get the others out of here. If I don't make it out I want you to find Torchwood in Cardiff. Ask for Captain Jack Harkness, he'll know what to do." Donna nodded her head. She stiffened, turning away from the Doctor.

"You heard the martian," Donna exclaimed, "Move." Donna nodded her head in the Doctor's direction in a 'good luck' gesture, before sprinting down the hall, Roc protecting her from flying bullets. Ama thanked the Doctor once more, before turning and running too. The rest of the alien group followed the escaping trio, all saluting or nodding their heads in the Doctor's direction.

The Doctor sighed, sprinting the other way, he looped around a corner dodging bullets and trapped doors. He stumbled to a halt. In his path, the group of guards he had heard laid unconscious. The Doctor raised an eyebrow at the scene before him. He felt a tingle in the back of his mind and immediately opened up to receive the telepathic message.

_I thought I'd give you a head start, _Ama stated in his mind, _Good Luck. _The Doctor grinned quickly sending back his thanks, before leaping over the fallen bodies and skidding to a stop at the next cell block. The door to the cell block was voice activated. A smirk settled on the Doctor's lips. One thing people didn't know about Time Lords were there uncanny ability to alter their voices, making them sound like somebody completely different. The Doctor concentrated on the voice he had heard the most. His tone changed, stealing Major Johnson's voice. He quickly stated the pass-code that he picked from Norris's mind. The emergency lights flashed wildly, turning the white hall into a dark red. The Doctor waited patiently, turning his head to the side and listening for any approaching ambushers. He finally heard a beep and the door slid open. Many of the alien's were already standing in anticipation, waiting to be released. The Doctor smiled enthusiastically.

"Which cell-block is this, then," He asked, as he rewired the system, quickly sonicing it with his device. The force-fields frizzed out and the alarms in the cell-block shrieked as the aliens were released. A slitheen approached the Doctor, her green fat jiggling as she stalked over.

"The testing block," she hissed. A few more aliens came bounding out, every single one of them weirdly shaped and different colors. "We're only used by the scientists, little man." The Doctor nodded his head, before quickly turning around.

"No time to chat," he quickly stated. He stretched his hearing, listening for the pounding footsteps of armed soldiers. He turned back to the group of aliens.

"Alright," He exclaimed, looking at the slitheen, "Can you get everyone out. I'll show you where the exit is." The slitheen nodded her chubby head, black eyes ogling the Doctor.

"Great," the Doctor lept forward, placing his fingers on the slitheen's temples and quickly transfering information to her. He pulled away and quickly jogged out the door. "Now run. Allons-y!" The aliens raced out of the cell-block and an ambush of bullets and soldiers attacked them. The aliens fought back, slicing their way through the onslaught of humans. They raced away, all following the slitheen.

The Doctor went the other direction, quickly stealing a pair of glasses from one of the fallen guards and a lab coat from a scientists that accidentally stumbled into the ambush as well as a pair of shoes. He pocketed the device he created and calmly walked passed guards, who didn't recognized him because of all the chaos. He quickly walked down the hall, straight face.

"Doctor," Somebody shouted behind him. The Doctor turned in surprise, facing one of the soldiers. The man had sweat dripping down his face and a look of panic in his eyes. How could this man know who he is? "Sir, you should find a safe place. Its not safe out here with all the aliens on the loose." The man glanced at him with concern and the Doctor sighed in relief. The young soldier believed he was one of the scientists. The Doctor cleared his throat, giving the soldier a sharp look.

"Are you telling me what to do young man," he stated, sneering slightly. He pointed his finger down the hall. "Down there, my life's work is in danger and I'm not about to let a bunch of escaped animals stop me from getting it. It might be destroyed." The Doctor glared, before turning on his heels and continuing his march down the hall. He felt a smirk play on his lips.

"Sorry sir," the young soldier stuttered out behind him. "I didn't know." The Doctor scoffed and turned a corner. And people told him he couldn't act. Eat your words Spielberg.

* * *

The Doctor opened up the next cell-block. He quickly ran in, zapping the controls with his device. All the force-fields fell with a zap. He could tell it was the supernatural block because each creature that exited, looked like they came from a child's nightmare. There were goblins and elves. Werewolves and fish-people and something that resembled a vampire. The Doctor recognized the werewolves snarling and baring their teeth at him. There long bristly tail's swinging back in forth. The only difference about these werewolves were that they were in the middle of transforming. They looked human but with wolf parts. The Doctor stood his ground. He held his chin high and in a loud, calm voice announced why he was here. "I'm here to get you all out. Either you can work with me or against. If you choose against you will be locked in here and never able to see the full moon again." The creatures glanced between one another, before the vampire approached him, his fangs glistening.

"How do you suggest we escape," he hissed between sharp teeth. The werewolves made no approach to stop him. "I doubt it is night." The Doctor lifted a brow, before shrugging.

"It is exactly 12:30 at night, but if you are still concern there's a sewer exit in the west side of the building. I'm sure you can escape and find sanctuary there." The Doctor glared at the supernatural beings. He stepped forward, his eyes threatening. "My only request, when I release you, is that you don't kill any innocent humans. I am giving you your freedom and in return please find another way to satisfy your diet." The Vampire nodded his agreement and the others soon followed. "I'll give you the information right now." The Doctor leaned over, placing his hands on the vampires temples and quickly sent all the information to him. The Vampire's eyes widened in shock, and a sly smile crossed his lips.

"I should of known you were a Time-Lord," he stated, "Your kind was the only type who would be able to create and manage such an elaborate plan." The Doctor stepped away, his eyes never leaving the vampires. He quickly pointed his device at the human werewolves, breaking their collars. The four breathed a sigh of relief as they slowly began to morph back to humans.

"Go," the Doctor commanded, "If you see others, release them." The supernatural creatures nodded and the Doctor sprinted out of the cell, barely avoiding being shot. He flipped and danced out of the way of the speeding bullets, running around another corner. He could hear the soldiers coming after him, but suddenly blood-curdling screams were heard and the Doctor knew the vampire and werewolves were dealing with the soldiers.

* * *

He raced through the labs, glancing through each window. He hadn't spotted any aliens or other creatures in the lab rooms yet, which made his job a lot easier. The Doctor skidded to a halt as something caught his attention. He walked back towards the door, peaking through the tiny window. Inside cooling shelves lined the walls, with tiny cylindrical tubes inside. But what caught the Doctor's eyes were aliens, who were trapped in cages to small for their sizes. The Doctor unlocked the door, using his sonic device and stepped inside. one of the creatures slowed her pacing, glaring at the Doctor.

"w-what are y-you," she hissed, "You're not one of the scientists." The Doctor shook his head, as he glanced around the room. The room was a lot larger than he expected and another door was at the far end. Cages lined the walls each with a different alien species. The Doctor looked at the cooling shelves, each shelf had a deadly pathogen, from earth or other planets.

"I'm here to get you out," The Doctor replied to the young alien. The alien perked up slightly, her pink hair turning a light purple. She frowned and shook her head.

"You can't," She stated. The Doctor spun, facing her.

"Why not?" he asked. He glanced over to the door, curiosity drawing him forward. He was already drawing to conclusions and didn't like where they were heading.

"Because we're diseased," she stated, "carriers. They have plans for us." The Doctor slowly moved towards the door, his hand reaching towards the knob.

"What plans?" The idea to what the plan was grew larger in his mind. He touched the knob and grunted, yanking his hand away. The doorknob was hot, a defense mechanism to keep people out.

"To send us home," she responded. She coughed covering her mouth. Her hair turned an icy blue. The Doctor stepped back, knowing exactly what was behind those doors. His face twisted in disgust, realizing the plan. He pointed the sonic device at the door, but nothing budged or shattered. Everything was locked behind a thick metal door. "You can't help us escape. We are contagious," the alien said, coughing, blood-spilled from her mouth. "You better run before we infect you too." The Doctor glanced back over at the aliens. They moaned in pain and he knew they were dying, slowly and painfully. He couldn't do anything about it, he backed out the door.

"I'm sorry. I'm so sorry," He said. He glanced at them guiltily, "I promise I'll help you."

The alien shook her head. "There's nothing you can do. Go. Help the others." She laid her head on the metal grating of her cage, bloody tears dripping from her eyes as she slowly died from the inside out. She had caught Frencidous, a deadly virus that was incurable. A virus that lasted for weeks killing its victim slowly and painfully. Many people did not survive from the deadly disease. He knew he had to stop them.

* * *

The Doctor ran. He ran down the halls, quickly glimpsing into each window and only stopping when he saw someone. He noticed a young alien chained to a table, scientists stood around him with notepads in hand and curiosity in their eyes. The alarms blared behind them, but the scientists paid no heed to the warning lights. The Doctor straightened the white lab-coat he wore and fixed his glasses and with an authoritative march he threw open the lab doors. The scientists jumped from the sudden bang and turned towards the Doctor.

"Excuse me," the Doctor said condescendingly, "What are you all doing in here? Do you not hear those alarms." The Doctor glared at each scientists, sniffing slightly. "Those are warning alarms for your information and whenever they go off it means _you..._" he pointed his finger at the scientists, wiggling it slightly. "Have to head for the nearest refuge." The Doctor threw his arms in the air in exasperation. "Do I see you heading that way? No!"

"But Doctor..."one of the men responded. The Doctor glared, sniffing haughtily.

"Smith." The Doctor replied, "Dr. Smith."

"It's just a few aliens that escaped nothing the soldiers can't handle." The Doctor scoffed in disdain, rolling his eyes.

"Just a few aliens he says." The Doctor glanced at the other scientists in shock at their idiocy. "I'll have you know its a whole bloody revolt out there and you're stuck in the cross-fire."

The Scientists glanced over at the door in shock, before the leading scientists began speaking again. "But the alien we're working on Dr. Smith..."

"Nevermind the bloody alien," the Doctor interrupted, glaring. "I'll take care of it. Do you want me to lose my job because of a few." The Doctor glowered at the men, pushing his glasses neatly up his nose. "Incompetent idiots refused to listen to my orders. Get out of here now before the fight comes this way!" The scientists immediately jumped into action, packing items away, and racing out the door.

The Doctor chuckled, before stepping over towards the young alien, who was tied down to the table. The alien was a rich, dark purple with bright yellow eyes and course black hair. Scales covered his skin and his nose was slightly turned up. He stared at the Doctor with fear and the Doctor understood how he felt. He had been on that table many times before with the exact same look in his eyes. Fearfully, waiting for the next cruel test the scientists would perform. The aliens lip wobbled and the word please left his mouth in a trembling mess. The Doctor gazed at him and softly quieted the young alien.

"Shhh...It's ok. I'm here to help," the Doctor calmly stated, "I'm the Doctor." The alien glared, his lips curving into a sneer.

"I know that," he spat, "Here to cut me open and pull out my insides are you?" The Doctor shook his head sadly and placed a consoling hand on the young alien's shoulder.

"No, I'm here to rescue you," the Doctor replied, "I'm as much a prisoner as you are." The alien's eyes widened and a happy smile played at his lips.

"You're the alien that organized the whole escape aren't you?" The Doctor nodded his head, unhooking the straps from the alien's wrist, legs, and torso. The young alien sat up and swung his legs over the side of the table, before quietly falling to his feet. He glanced up at the Doctor, smiling. "I'm Tak by the way." The Doctor bobbed his head in greeting, before turning around and looking out the door. No one was outside. He looked back at Tak.

"Ok Tak. What I'm going to do is give you instructions on how to get out of this place. When you escape, look for a red-headed woman named Donna. She'll be taking you to a safe haven until I can get back to you guys and take you all home." Tak nodded his head in understanding and the Doctor leaned down placing his fingers on Tak's temples, quickly sending all the information he had found into Tak's mind. Tak's eyes widened with surprise, before nodding his head. The Doctor stepped away, looking out the door to make sure the coast was clear. He waved his hand and Tak followed him over. "Be wary of traps," The Doctor stated, "I've been able to avoid a few, but that's because I know where they are at. Just run. Run and never see this place again." Tak nodded his head, before saluting the Doctor in his own alien way.

"Thank you Doctor," He said, "I will one day find a way to repay you. I promise." The Doctor shook his head, pushing Tak out the door.

"No need," The Doctor answered, "I do this for a living. Now go. I don't want to rescue you again." Tak smiled, saluting once more before he sprinted in the direction of the exit. The Doctor took one more look around, before sidling out and heading the other direction. Shoving his hands into the coat pocket, he swiftly walked down the hall turning a corner.

* * *

Time was running out and he knew it. He didn't know if any more aliens were down this ward or another, so he did something he hadn't done for years. He stretched his mind out to every living organism in the building, hoping to catch a cry for help. The task was difficult while moving, most Time Lords had to meditate to perform this psychic feat. But in the Doctor's case, sitting and meditating was not an option. He touched the minds of every person in the agency. Every guard, scientist, technician,prisoner, and animal but he couldn't hear any psychic cries for help. The one thing he did hear was the TARDIS.

The Doctor's eyes snapped open when he realized the TARDIS was a prisoner here as well. Her cries for help and for her thief brought tears to his eyes. He knew she was brought here, but to hear her screaming in pain was unbearable. He hadn't heard her scream like that since the Year That Never Was. He knew what they were doing to her. They were trying to crack her open, enter her. Mess around with her circuits. But she was fighting back, refusing to allow them entry. So, they tortured her. His teeth gritted in anger at the psychic screams of distress. He marched forward, listening to the directions she was giving him on her whereabouts. He forgot about the plans of getting to the control room and shutting everything down. All he could think about was his TARDIS. His longest companion and best friend. He knew he should of stuck with the original plan, but how could he when someone he cared about needed him.

Somebody fell backwards as he crashed into a petite body. He stumbled back slightly and a soft 'oof' left the person's mouth. He glanced down and begun backing away slightly. The girl's green eyes widened in recognition and she quickly got to her feet.

"Subject 13," she said. She opened her mouth widely. "Help! I found it! It's over..." The Doctor lept forward, covering her mouth. He stared at her pleadingly and she fought back, trying to push him away. Her voice muffled by his hand.

"Please, Claire," The Doctor whispered, "Just let me go. This place is wrong. What you are doing is wrong." Claire lifted a skeptical eyebrow, glaring at the Doctor. Her screams and ranting muffled by his hand. "Look at what you people are doing. You're locking up innocent lifeforms and experimenting on them, while others are transformed into killers. Assassins to perform the dirty work you humans don't want to do. If you have any kindness or morals in your heart you would let me go." The Doctor could hear the fast clomping of metal shoes on the white-floor. The Doctor glanced down the hall, panic in his eyes. He didn't have time for this. He looked back at Claire, who was still glaring at him. "I promise you if you help me this one time, I'll get you out of here. I'll find you a nice job where you can actually help people. Whatever you want. I've seen the real you, Claire, when I was on the floor bleeding. You were kind to me and patient. Something I hadn't experienced in a while. Just help me one last time." Claire lifted a quizzical eyebrow and nodded her head.

The Doctor smiled and removed his hand, just as the group of guards appeared. The Leader of the group stepped forward, tranquilizer in hand.

"Is everything alright ma'am," The leader asked, "I heard a scream for help. Did you find one of the aliens?" Claire shook her head and the Doctor put his best concern look on.

"Aliens here," the Doctor exclaimed, "Nah, I heard her scream and thought she was in danger. I was going to help her back to that safety room, you have set up, because she was a little weak in the knees." Claire nodded her head, shaking slightly.

"I was just spooked," she answered the guard, "I thought I saw one." She swallowed, looking around fearfully, "All these blaring lights and guns. I just don't handle high-pressured situations very well. If it wasn't for Doctor..." She glanced over at the Doctor, asking for help.  
"Smith," the Doctor responded politely, "Dr. Smith." Claire nodded her head.

"If it wasn't for Dr. Smith here, I might of collapsed from fright," She lied, placing her hand on her heart. The guard glanced over at the Doctor suspiciously.

"I've never seen you around here before, but your face seems familiar," The guard stated. He glanced the Doctor up and down and the Doctor plastered a smile on his face, rocking on his heels.

"Oh, I was hired yesterday," he responded easily, "With the amount of new aliens coming in, they needed another Doctor. And as for familiarity, I just have one of those faces. A lot of people say I look familiar." The Guard stared at him skeptically, before nodding his head in agreement.

"I apologize for the accusation Dr. Smith, you can never be too careful. I'm sorry your second day hasn't been what you expected. Normally these creatures are locked up. I guess it's just a bad day."

The Doctor waved his hand unconcernedly. "Meh...It happens. I wish you luck in your captures. Me and Claire will head down to that protection room if you don't mind. I don't feel like dying in a crossfire on my second day." The Doctor smiled disarmingly, before looping his arm in the crook of Claire's. "Come along Claire, these men have a job to do." Claire nodded her head and stumbled along with the Doctor before they turned a corner.

She turned around, smacking the Doctor's arm and glaring."You are such a liar," she spat. The Doctor glanced at her, taken aback.

"What did you expect me to do," he retorted, "Say 'hey I'm the alien that escaped and let loose all the other prisoners. Arrest me please.' I don't think so. I believe that would be a terrible ending to my plans." Claire glared sharply at him, crossing her arms. Her black hair was pulled back into a ponytail.

"If I get in trouble, I'll haunt you for the rest of your miserable life," She threatened. The Doctor shrugged.

"I can live with that," he retorted, "Thanks for your help. You're not a bad actor." He smiled brightly. Her glare dropped and she couldn't help but grin back. The smile was infectious. Her grin dipped and she leaned against the wall, placing a hand on her forehead.

"I can't believe they fell for it,"She exclaimed, "It was so simple yet brilliant." She rubbed at her face, sighing. The Doctor peaked around a corner, before stepping away as several armed men ran past them. "God, The Colonel and everyone else was right. Aliens are manipulative and tricky." The Doctor shook his head.

"Nah, that's just me," he responded, seemingly more focused on the door across the room. Claire rolled her eyes.

"How could they even believe that blatant lie," she questioned, "I wouldn't of believed it." The Doctor glanced over, smiling.

"I have an honest face," he replied simply. Claire glared, before her lips begun to quiver in laughter.

"You're mad,"She blurted out, her laughter growing more hysterical. The Doctor chuckled, before turning his gaze back over to the door on the other side.

"Yep," he agreed, popping the p, "Madman with a box. That's what I am." He watched several more groups of soldiers run pass, before turning back over to Claire. Her eyes had a familiar glint in them. A glint that he had noticed from Martha and Rose while they traveled with him. What was it with human women? "I think you should get going," he stated, "I don't want you to get in trouble or stuck in the middle of the search. This is where I say goodbye."

"Where are you going," she suddenly asked. She seemed to snap back into reality, realizing the dire situation they were in. "You can't. If they find you, they'll hurt you. I know where the exit is. I can take you there."

The Doctor shook his head. "You've been helpful enough Claire and I don't want you to get into trouble. I'll be fine." Claire nodded her head solemnly. "Head back to wherever the safe room is or whatever you call it. I promise when I escape I'll come back for you and find you a job where you can exercise your full potential." Claire looked down, before her eyes widened with realization. Her head popped up and her mouth curved, forming words silently before she coughed and tried again.

"I didn't even get your name," she stated, "I mean I gave you mine but I never thought you had a name until now. I always thought you were just subject..."

"The Doctor," he replied, "I'm called the Doctor." he looked out once more, noticing all the guards were gone. He smiled warmly at Claire. "Thank you Claire and live to your full potential. I suggest you leave this place. It has no use for you." The Doctor winked and sprinted out of his hiding place. Claire watched him run, before nodding her head and quickly walking away.

The Doctor stepped over to the door, looking back and forth quickly, before pulling out the sonic device he created. He cranked the lever and the device begun to buzz. He pushed it against the control pad, but it was deadlocked. He tried voice activating it, using every voice he heard in this place. But it kept blaring in bright red letters, access denied. He tried to break into the control pad and rewire the whole database and information, but instead it shocked him. The Doctor shook his hand and growled angrily, banging his fist against the door. He could hear the TARDIS screaming on the other side. He tried zapping the knob, but nothing budged. He slowly backed away from the door. He would have to come back for her. He stepped back. _Click._ He heard several guns behind him and a slow sarcastic clap. He slowly raised his hands, turning around to face ten armed guards and Colonel Graham. The Colonel's lips curved into a cruel smile and the Doctor held his head high, defiantly and bravely.

"Impressive," the Colonel stated indifferently, "Until now and to think you would've gotten away with it if you didn't go looking for your ship." The Doctor glared, his hands still in the air. His fingers twitched slightly, as he organized his thoughts, thinking up his next attack. He was cornered, unable to move freely with ten guns pointed at him. Meh...He'd been in worse situations. He smiled disarmingly, stepping forward slightly. Immediately someone shot a warning bullet and the bullet blazed past him, hitting the wall. The Doctor gulped. Ok, not a good idea to move. "And tricking my staff," the Colonel exclaimed, "by pretending to be a doctor. I'm going to have to fire those fools for believing such a ridiculous story and the only way out..." The Colonel moved a finger across his neck.

The Colonel pulled out a tiny gun from his holster and pointed it at the Doctor. "I think its time to say Good Night, Subject 13." _BANG._ The Doctor fell to the floor, three needles protruding from his neck. Colonel Graham holstered his gun and turned from the guards. "Get rid of the labcoat, shoes, and glasses and whatever else you find on it." The Colonel glanced down at the still body of the Doctor. "Take it to the interrogation room, before continuing your search for the others. I want that _thing_ punished." Contempt and disgust dripped from the Colonel's lips when he said thing. His lips were quirked up in a sneer and his black glasses, over his eyes, flashed from the red siren lights blazing overhead. The guards said a quick 'yes, sir' before hoisting the Doctor up and dragging him out of the hall. The Colonel turned on his heels and marched away. Alarms screamed in the background and a constant female voice repeated 'prisoner has escaped.'

* * *

**I hope you enjoyed that chapter and thanks for sticking with me for this long. Yep, the story is not over yet. Several mysteries are still on the loose, but I'm sure many of you are starting to put at least one or two of them together.:) I believe there will be about 10 to 12 more chapters of this story. So, yeah hope you guys keep following and reviewing. The good news is Captain Jack Harkness will be in this story because I absolutely love him and he always comes to the Doctor's aid. The bad news is the Doctor is still trap, but these next few chapters will be more focused on the mystery and the rescue team then actual whump. Don't get me wrong, it will still be in there just not as the main focus. So, yeah please keep reading and reviewing and hopefully you stay interested. Thanks again for all the wonderful feedback. :)**


	32. Chapter 31

**Thank you for all the wonderful reviews. :) Here's the next chapter. Please review some more and tell me what you think. **

Chapter 31

The doors slammed open and Colonel Graham stiffly marched into the interrogation room. His jaw was tight and he looked ready to murder anyone who got in his way. Two guards were standing off to the side, while another two were happily delivering the Doctor's punishment. Colonel Graham halted his stride, standing tensely next to Major Johnson. Johnson impassively watched the Doctor's beating as the Time Lord cried out in pain.

_Swish-Crack!_ "Nuahhh!" A thousand sharp needles shot up the Doctor's back as the electric whip slashed across his back once more. The Doctor gritted his teeth, squeezing his eyes tightly shut. The first thirty minutes he took his punishment quietly, only moaning once in a while. He didn't want to come across weak or soft. But they had switched the whips direction and now the lash opened up the wounds deeper.

The Doctor slumped against the chain that held him up in the air. The metal cuffs were locked around his wrist, stretching his arms over his head. While another pair of metal cuffs were locked around his feet, so he wouldn't swing back and forth. The Doctor dazedly glanced up, making eye contact with the Colonel. His face peppered in bruises and his skin covered in slash marks and burns. The Doctor glared, giving the Colonel a slight smirk. He knew why the Colonel was angry.

_Swish-Crack! _"Arrrgggg!" The Doctor threw his head back, as another shot of agony ran up his back. The Colonel threw up a hand, halting the punishment. The torturers lowered their weapons, stepping back from their victim. The Doctor breathed heavily, slumping slightly in the chains. His head lolled to the side and he laughed. He knew if he laughed, he wouldn't cry.

"Missing a f-few prisoners," he sarcastically stated, blood dripped down his mouth. His laughter grew more desperate and hysterical. He gritted his teeth as pain shot up his back. Colonel Graham sneered, his jaw tightening in hatred. He marched forward, lifting his hand. He backhanded the Doctor across the face. Blood flew from the Doctor's lips and his head snapped to the side. He groaned, but rough fingers dug into his cheeks, yanking his head up. Sour, hot breath and the smell of gin touched his nose. He was forced to make eye contact with the Colonel.

"Where are they," the Colonel growled, spittle splattered the Doctor's face and his cheeks were squeezed tightly.

"I d-don't know," The Doctor replied, a cheeky smile playing at his lips, "I didn't want them to tell me in case something like this happened. I'm as much in the dark as you." The Doctor gasped as he was punched in the kidneys. His back arched, mouth gaping. Rough fingers grabbed his face once more.

"Every last one of them escaped," the Colonel hissed, "except for you and those sick freaks. Those animals belonged to me." He shook the Doctor a bit, getting into his face. "I could charge you with thievery but then again you belong to me. So I guess I'll just punish you for your disobedience." A cruel smile twisted his lips. "And I have a lot of plans for you." The Colonel released the Doctor's face and stepped back. "I guess your plan failed because I still have you." The Doctor glanced up and quirked an eyebrow.

"You said that all the others escaped correct," the Doctor replied. The Colonel stiffly nodded his head. A grin spread across the Doctor's face. "Then I guess my plan was a success." The Colonel sneered in disgust. "My escape would've been a bonus anyways." The Colonel turned away from the Time Lord, facing the guards.

"Take it down to room two," he stated, "Me and the Major have a little surprise for it." The Colonel marched out of the interrogation room with the Major behind. Two of the guards stepped forward, unchaining the Doctor. The Doctor fell to the ground, smacking his knees on the hard floors. Agony shot up his leg and he gritted his teeth, groaning. The Guards grabbed his arms and hoisted him to his feet. They dragged him out of the room and down to room two.

* * *

The Doctor was led into a medium sized room. The walls and floors were gray and in the middle was a table with two chairs. In one chair a figure sat, with colored paper spread across the table. The figure wore a beanie. A beanie The Doctor would recognize anywhere. His hearts jumped to his throat, as he was dragged across the floor and shoved roughly into the second chair across from the man. Bobby.

Bobby sat, fiddling with his fingers with an innocent look upon his face. There was worry behind Bobby's eyes but when he saw the Doctor all that worry vanished because he knew the Doctor was here to save him. Bobby frowned, spotting the Doctor's bloody and bruised face. His eyes were filled with sadness and a tint of guilt that confused Bobby very much. Why would the Doctor feel guilty? He got everyone out didn't he.

"Bobby." Bobby's ears perked up to the sound of the Doctor's scratchy voice. His voice sounded raw and swollen, like he had been screaming for hours. "Why didn't you leave?" Bobby's eyes shot back over to the Doctor and he smiled, before placing a consoling hand on the Doctor's bruised wrist.

"I did Doctor," Bobby responded, "But one of the guards saw me leaving and he told me you were hurt. I had to come back." Bobby's eyes grew very serious, his eyebrows scrunched in concentration. "Those scientists don't know how to take care of you properly. I was scared you were throwing up and sick in bed again." The Doctor's brown eyes darkened with depression. He felt an emotional lump form in the back of his throat.

"B-Bobby. I told you to leave," the Doctor said, "I told you to run and never look back." The Doctor's shoulders quivered with uncontrolled emotion. "W-Why didn't you listen to me. Why did you have to come back and care about me. About my well being. About anything." The Doctor felt the rage and raw emotion boil in his stomachs and burn his throat. Why couldn't life be fair?

Bobby glanced down at the table and his bottom lip quivered."I'm sorry Doctor," Bobby stated. He rubbed a tear from his eyes as his glasses began to fog up. "Are you mad at me? Am I no longer your friend." The Doctor bit his bottom lip and leaned his head against the table. The Doctor shook his head bitterly, he heaved deeply, and lifted his head. His eyes were red from unshed tears.

"No," the Doctor said simply, he brushed a hand across his eyes, not caring about the painful bruises or cuts. "I can never be mad at you Bobby." Bobby seemed to brighten slightly, a small smile curving his lips. The Doctor felt another gasp of pain and guilt hit him like a punch to the face. Why were they doing this to him? How could Bobby not fully sense the danger he was in?

"Are we still friends, Doctor?" The Doctor glanced up, before lowering his gaze unable to look Bobby in the eyes without a wave of guilt. Bobby watched him expectantly, waiting for an answer.

"Always," the Doctor whispered, wiping a tear from his eyes. "Always Bobby Mills. No matter where I am at, I will always be your friend." Bobby smiled at the response, though his eyes still held the concern he felt towards the Doctor. He had never seen the Doctor so beat-up and depressed or maybe he had and just didn't remember it.

"Doctor," Bobby stated. He gave the Doctor a very sympathetic look and a kind smile. "It can only get better. Remember that." The Doctor nodded his head, a fresh onslaught of tears rolling down his cheeks.

The Doctor turned his head, to the heavy marching of steel boots. Major Johnson bent down to eye level, a cruel smirk on his face. His cold eyes sending all the hatred he felt for the Doctor. "Why don't you teach Bobby here how to make a new origami animal," the Major growled, "I'm sure he'll enjoy that. We don't want all this nice paper to go to waste." The Major stiffly stood up and walked over to the side of the room. He crossed his arms. "Go on," he mockingly ordered, "Ask what origami animal he would like." The Doctor glanced over at Bobby, clearing his throat.

"B-Bobby w-what t-type of origami animal would you like," The Doctor asked. He shakily reached for the blue paper, handing one to Bobby and keeping one for himself. Bobby glanced over at the Major, fear now evident in his eyes.

"A c-crane," Bobby said. He gulped loudly and begun folding his paper. The Doctor nodded his head, his hands shaking and crumpling up the blue paper.

"Of course," the Doctor replied. The Doctor took a nervous glance at the Major, before switching his eyes to the paper in his hand. He chewed on his lip as he folded the paper over again.

_Bang. Thump. _The Doctor jumped out of his seat, when Bobby's head smacked the table, blood seeping from the back of his head and soaking his beanie. Bobby's eyes were lifeless behind the round specks and his mouth gaped, blood flowing from between his lips. The Doctor's mouth gaped in shock and his bottom lip quivered from witnessing his friend's life being stolen. Why? The Doctor fell back into his chair, tears spilling and nose runny. "I'm so sorry Bobby," the Doctor sobbed, "I failed you." He glanced over at the man who killed Bobby Mills. His hearts burning with anger and slowly crumbling at the loss of a dear friend.

Major Johnson holstered his gun and silently marched over to the Doctor. The Doctor was stroking Bobby's hand and mumbling to himself. His eyes were clouded, unfocused and he seemed to be far away from reality. The Doctor repeated 'I'm sorry' like a broken record. The Major stared down the Doctor, trying to gain his attention.

"See what happens when you make friends," the Major mocked, "They die. Especially when they are traitorous to the agency they work for." The Doctor didn't answer. His whole focus was on the dead Bobby and trying to will him back to life. He never asked for Bobby's forgiveness for putting him in this mess and now he never could. The Doctor rocked back and forth. He was so selfish, only caring about himself and he put the people he cared about in danger. The Major was right. Whenever he made friends, either their lives were ruined or they died to help him. The Doctor lowered his head, his hearts breaking. He let out a strangled cry of anguish. He glanced up at the Major, his eyes blurry with tears. He lips trembled with anger and he gritted his teeth.

"I'm sure this makes you angry enough to kill," The Major sneeringly stated, "To break the neck of the man who caused your friend's death." The Doctor glared up at the Major, his eyes darkening with fury. His fist balled up and his back straightened stiffly, a quiet dark mantra in the back of his mind continually said 'kill him. He deserves it.' The Doctor pushed back the growing dark bubble as it grew louder in his head, telling him he was the last of the Time Lords, the Time Lord Victorious. He had the right to decide who lives and who dies. To be their judge and sentence their punishment. The Doctor growled darkly, clutching his head and the chant grew louder. He kicked out, screaming in pain and rage. He finally flew out of his seat, slamming his fist on the table.

"STOP IT!" He shouted. The noise died and his head once more a stifling silence. A constant reminder of the absence of his people. He fell back into the chair, exhausted. The Major had taken a couple steps back, startled from the Doctor's sudden outburst and the chilling energy that emanated from him. The Doctor breathed heavily, slowly trying to calm his nerves. He gulped and glanced up at the stiff Major. Closing his eyes, he pinched the bridge of his nose, swallowing heavily. He popped one brown eye open and then the second, staring at the Major unemotionally. He sat up straight and leaned his elbows on the table.

"I will not kill," he stated, "No matter the reason. I cared about Bobby, but if I killed you that would bring me down to your level. I am not a monster." The Doctor leaned back and stared at Bobby's motionless body, his bottom lip trembled. He had a whole list of 'If onlys' but he knew if he thought of that list it would cause him to spiral down a dark path that would consume whats left of his soul. He would not allow that. The Doctor looked up at the stone-faced Major, scoffing. "You call me the monster," he stated, "but have you looked in the mirror lately. Bobby's blood is on your hands and no one elses. You killed an innocent man in cold-blood in an attempt to hurt me. Congratulations, you have. But now Major Johnson you have unleashed the beast and it won't rest until this organization is erased from the universe." The Doctor stared, determination radiating from his eyes and it sent chills down the spines of everyone in the room.

Colonel Graham stepped forward, arms crossed behind his back. He eyed the Doctor coldly, before waving two guards over. "Take subject 13 to isolation. It can think about what it has done for the next few days. No food or water for at least a week." The two guards yanked the Doctor to his feet, holding him up right. Colonel Graham glanced down at Bobby's body, he sneered slightly. "Get rid of the body."

The Doctor gaped,struggling in the guards arms. He did not have the energy or strength to break free. "You can't," the Doctor shouted, "You can't just dump his body somewhere. Send Bobby back to his Mother's. Let her know what happened." The Colonel turned quickly around, facing the Doctor.

"That an alien killed her son," he sneered. The Doctor lowered his head slightly, trying to contain his anger. The Colonel smiled, misreading the look as properly cowed. "Yes, I think that's what I'll do. Most people are already afraid of extra-terrestrial lifeforms. Thanks to the last few events. It would be an easily believed tale." Graham glared at the Doctor, before waving his hand dismissively. "Take it away." The Doctor was dragged out of the room.

He was taken to a small room down the hall and in the middle of the room was a metal box. One of the guards stepped forward unlatching the box and opening it widely. They pushed him roughly into the box, locking it tightly, before walking away.

The Doctor sighed, curling in on himself. The box was only big enough for him to sit in, with no elbow room at all. He was forced to bend his head down and sit in a squatted position. The box was completely black and he couldn't even see his hand, even with his superior eyesight. Since he was alone, the Doctor began thinking up escape plans. Plans that would break down the security system of the Underground and plans that would end this evil agency once and for all. But right now they were just plans and they wouldn't be put into action until he was released from the box. He just hoped he wouldn't develop claustrophobia.

* * *

A purple eye popped open, as Ama heard someone rustling around. She slowly sat up from the mat she slept on in the warehouse that Donna had found. She heard the soft snores of many of the aliens that were released yesterday and she smiled happily. She couldn't believe she was finally free. After three years of torture it was like a wonderful dream. She caught a flash of red and immediately knew who was up.

"Donna," Ama asked sleepily, she stretched her limbs and watched the red-head busily moving around among the other aliens. Donna had been magnificent. She had found the warehouse and had set it up as a sanctuary, before sending Ama out to direct runaway aliens to the safe haven. Ama had used her telepathic abilities to alert all the ex-alien prisoners to the warehouse.

Donna had also discovered they were in Birmingham and that they had exited a large office building, that seemed relatively innocent until you went underneath. None the less, as more aliens straggled in, Donna continued to fret. She searched for the Doctor among the aliens, but no one could find him. Ama had comforted Donna, telling her to be patient and that everything would work out fine. But that did not calm her nerves, Donna continued to grow more antsy, fearing the worse. Ama sighed, watching the fiery ginger bustle about and pack items. "Donna what are you doing?"

Donna turned a determined gaze on Ama and Ama jumped from the sudden fire in her eyes. "I'm going to Cardiff. It takes around two hours to get there, if there's no traffic or other obstacles. I'm going to look for this Captain Jack fellow." Donna begun packing a knapsack. The one useful thing about this warehouse, was that the crates were filled with clothes and blankets, apparently it used to be a storage facility for fabric goods until it was shut down.

"Why,"Ama asked. Donna turned to her, gaping, staring at her like she was the biggest idiot she had ever laid eyes on.

"Have you noticed we're missing someone rather important," Donna sarcastically stated, "and that someone saved every single one of you." Donna placed her hands on her hips. "How about you ask me why again. See if you can figure out the answer."

Ama lowered her head, guiltily. She was worried about the Doctor too, but expressed it a little less then Donna. "Sorry." Donna rolled her eyes and continued packing.

"I need to find Torchwood,"She said, "Getting to Cardiff will be easy, finding the stupid organization will be hard." Donna huffed, looking through the boxes of clothes and other nick-knacks hoping to find something important. "It's probably underground," she grumbled, "Maybe I'll bring a shovel." Ama rolled her eyes and settled back on the mat, her stomach growling with hunger. Donna glanced over at her and smiled softly. "Hungry,"she asked. Ama nodded her head. "Maybe we'll find something to eat."

"Donna maybe you should wait a bit," Ama proposed, "at least until morning." Donna shot a glare in Ama's direction.

"I'm not waiting any longer sweetheart," Donna stated, "I've waited a full day for him to show and he didn't. Now it's time to find his friend." Ama groaned, there was no reasoning with this woman. She stood up and stretched.

"Fine," Ama stated, "I'm coming with you. You may need the company and I want to help the Doctor as much as you do." Donna stared at her and shook her head.

"No, Ama," she said, "I don't think its safe for you. I mean you're a little...blue." Ama glared at Donna and crossed her arms.

"I'll wear a hoodie then," Ama retorted. She strode over to one of the bins, looking for a hoodie. She pulled out a bright pink one and pulled it on quickly, throwing the hood over her head. "Ta-da!" She threw her hands in the air. "I'll find gloves or keep my hands tucked into my pocket the whole time. I'm going with you and that's final." Donna nodded her head and shrugged.

"Not arguing with you," Donna replied, "But you have to stick close to me. I don't want to lose you."

"We should let the others know we're leaving,"Ama stated, "So they don't wake up scared when they find us missing." Ama and Donna jumped when they heard a loud snort, Roc cracked an eye open and glanced over at the two women.

"Where are you going," he muttered sleepily. He turned over on his mat and quickly sat up.

"To Cardiff," Ama replied, "to find the Doctor's friend." Roc nodded his head sleepily.

"Good luck then," he stated. Donna kneeled down next to the sleepy alien and eyed him seriously.

"Roc, can you tell the others where we're going," she asked, "I don't want them to panic when they find us missing." Roc bobbed his head, yawning. Donna smiled and patted him on the shoulder friendly. "Thanks." She stood up and glanced over at Ama, who waited at the warehouse entrance. "You're in charge when we're gone," she added.

"Ok," Roc mumbled, before falling back to sleep. Donna jogged over to Ama and they both headed out the doors of the warehouse, starting their new journey to Cardiff.

* * *

**I hope you somewhat liked the chapter. I am sorry to those who liked Bobby, I had already decided that Bobby was going to die in the story and it didn't work out any other way. I honestly loved Bobby and killing him made me really sad. I had a difficult time writing that scene. But I needed something that would almost unleash the Time Lord Victorious and that's what I believed would cause it. But the Underground now has no leverage over the Doctor. He won't be as willing to work with them, now that they had killed one of his friends and Donna has escaped. He can fully focus on shutting the place down and solving the mystery. I hope you keep reading and reviewing because now Donna is off to find Captain Jack. :) These next few chapters will be switching between the Doctor's captivity and Donna's journey. Please review some more and tell me what you think. :)**


	33. Chapter 32

**Thank you so much for the reviews! I am glad you all love this story. Sorry, I didn't update yesterday, but I had a job interview and I needed to prepare for it. I can happily say I am now employed. :) Thank you again and here's the next chapter. **

Chapter 32

"The words 'I told you so' just doesn't seem to quite cut it," Dr. Morley stated, a small smirk quirking at the corner of her lips. She stood in Colonel Graham's office, leaning over his desk. The Colonel growled at the mockery tone Dr. Morley had put on. After Dr. Morley's first test with subject 13, she had arranged a meeting with him and voiced her concerns about the alien's intelligence. She told him that she believed subject 13 would try to escape, but he brushed it off as paranoia. Quite surprisingly, it escaped that night, letting loose all the other prisoners. Utter chaos ensued the rest of the night, until they finally caught the alien responsible. Every alien they had escaped and were now loose in the city.

"How was I suppose to know that subject 13 was building some alien device right under our noses," the Colonel growled, "It never did anything and it never showed the intelligence to completely put a plan this elaborate together." Dr. Morley crossed her arms and raised an eyebrow. Her look purely stated 'you're an idiot.'

"Did you not read the files on subject 13," she asked condescendingly, "or did you just skim through them. Because I most certainly did read the files and everything pointed to extremely clever and manipulative." The Colonel's lips curved in a sneer, but he did not answer. He leaned back, waiting for Dr. Morley's rant to continue. "You know, you could of looked at the video footage more often. It just proves how incompetent our surveillance team is. Think about it. Subject 13 was making friends with staff members and the other prisoners, manipulating them into helping him. It got to the point where even our ex-janitor believed he was its friend."

Dr. Morley paused for a second, crossing her arms, and letting the information sink in. The Colonel's eyes clouded with anger. He was going to fire the whole damn surveillance team. How dare they not pay attention to the footage. This whole crisis could have been averted if they weren't incompetent. Caging these freaks was enough work, he didn't need to deal with idiot employees. "And because of this," Dr. Morley continued, "He built a highly affective weapon right under our noses and almost brought down our security system." Dr. Morley slammed her fist on the table, fire in her eyes. She wanted the Colonel to understand how close they were to being destroyed.

The Colonel glanced up, a sneer on his lips. He hated being talked down to, but Dr. Morley had a point and it was no use getting angry at her. It was his own arrogance and trust in his team and defense systems that allowed the aliens to escape. He should of known they would plot something like this. Aliens were traitorous to the people who took care of them. They should have been thankful to him for giving them a place to sleep and providing them with food and clothes on a world that wasn't so forgiving to their kind. Backstabbing animals, always needed to be taught a lesson. Pretty soon there wouldn't be any use for them, if his plan worked out right. But he still considered keeping the Time Lord. It might be useful to his goals as a backup plan. Besides, it was nice to gloat about taking down the last of a powerful race and using it as a pet. Attack dog maybe. The Colonel glanced over at Dr. Morley, who still leaned over his desk with a threatening look on her face. It was obvious she wasn't pleased with the outcomes of the escape. She had lost valuable specimens too.

"Well, What are you going to do about it," She questioned. She glared at the Colonel, waiting for an answer. She knew she shouldn't talk to her boss in that tone, but she was pissed. Yes, she still had all the data she obtained from the aliens, but she would never be able to cross reference it or redo the tests again because of the Underground's stupid mistake.

Colonel Graham glanced up, a snarl rumbling from the back of his throat. He leaned forward, glaring at Dr. Morley. "I'll tighten security," he replied, "Put in more surveillance cameras, guards 24/7, I'll even strengthen the force-fields." He slammed a fist on the table. "And If I have too, chain the damn freak to its bed, so it can't move. Feed it through a damn IV if its needed. Overall, that animal is not escaping again." Dr. Morley raised an brow.

"Those are all extremely brilliant plans, Colonel," she stated, "And something we should definitely consider. If it escaped once, it will try again. But I have a better solution." Dr. Morley pulled out a small box and slid it over to the Colonel. The Colonel opened the box, pulling out a metal collar.

"Collar it," he stated, a grim smile pulled at his lips. He should of collared the freak long ago. If you didn't know what the alien was capable of, always go the cautious route. That's what he did with rock monster they captured. But then again, the rock monster was physically powerful while subject 13 was more cleverly powerful.

"The scientists have designed the collar to latch onto to subject 13's DNA and shut down or weaken its physical strengths,"Dr. Morley lectured, "But it won't affect its intelligence. We will be able to control subject 13. Switch on and off its abilities and give it a shock whenever it misbehaves. We're in the process of installing a detonator in the collar. The collar will act like a leash. We can put in how far it could move. Lets say four feet. If we tell the collar it can only go four feet in either direction and Subject 13 crosses that four feet marking it will give him a powerful shock that would knock him unconscious or if it continues to move, the collar will blow its head off. Which personally I don't believe it would try to risk getting its head blown off. Its survival instincts are to strong." Colonel Graham's eyes widened at the prospect of the little collar in his hand, it would definitely make controlling Subject 13 easier. Dr. Morley took the collar from his hands, placing it back in the box. "But the collar is still in working progress and won't be of use for a bit longer." The Colonel nodded his head and cleared his throat.

"Are you planning on using it," He asked, pointing to the box. Dr. Morley gave him a disgusted look and sniffed.

"Of course not. I despise violence," She stated, "I believe the only way to get these aliens to cooperate is to treat them with a bit of respect. But most of you are so skittish around them, deciding they need to be controlled to be cooperative. Hence, the building of this deathtrap."

The Colonel nodded his head, leaning back slightly. Things were actually looking up, which was a surprise considering yesterday and today. "Dr. Morley. I was wondering if you would like to continue your studies on subject 13. Talk to it. Maybe learn a bit more about its personality and report back to me. I believe the more we know about our trouble-making recruit, the easier it would be to control it. You seem to be able to read into its persona a lot better then anyone else. Plus, you're the most patient when dealing with these freaks..."

"Basically you want me to be subject 13's psychiatrist," Dr. Morley interrupted, "And report back when I notice something interesting or possibly helpful. Correct?"

The Colonel nodded his head. "Correct." Dr. Morley put the box back into her lab coat pocket and nodded her head.

"Fine I will do it," She stated, before a questioning gaze settled on her face. "Colonel Graham, sir. Have you noticed some of our staff went missing."

"There was a lot of deaths, Dr. Morley," he replied, "Those animals ripped most of my men to shreds."

"But, Colonel," she continued, "Some of the people who went missing weren't found among the bodies."

"Like who," the Colonel coldly asked. He didn't like backstabbers and if it meant some of the staff decided to flee during the massacre, then he was going to find and kill them. He didn't have time for cowards.

"Claire Michaels, sir," Dr. Morley responded, "A young physician, who cared for the aliens when they were injured. She disappeared right after the battle and never returned. In fact, she seemed to have dropped off the face of the Earth."

"How do you know this, Morley," he asked, his muscles seemed to tense in anger. Dr. Morley cleared her throat.

"I was walking to her medical station and was about to knock on the door, when I heard a strange groaning sound," Dr. Morley explained, "I opened the door and Claire wasn't there. When I specifically saw her five minutes ago walking into her station."

Colonel Graham grunted, before waving his hand in dismissal. "I've got important work to do, Dr. Morley. I can't be concerned with conspiracy theories." He turned away, pulling out one of the files, in the stack on his desk. It was always terrible dealing with paperwork after an escape, let alone three to four cell-blocks worth of escapes. Also, needing to write letters to the families, informing them about the death of their child was never easy either. The Colonel glanced over at the family picture that sat on his desk and his eyes grew sad. In the picture, his son and daughter smiled brightly at him and his beautiful wife with her long blonde hair. He sighed, and rubbed his eyes that were covered by the sunglasses. Their lives were taken so suddenly, all because of a stupid tin-can and a cowardly alien that refused to help them. He couldn't even protect them. He ran. When his family was murdered, he ran. He didn't try to defend them or fight. He ran like a coward and that was unforgivable. His knuckles turned white as he clutched his hands. It was those aliens fault. If they never existed, his family would still be alive. He heard the soft closing of the door, as Dr. Morley left his office.

The Colonel's teeth gritted, as he glanced over at the trophy case he had in the corner of his office. One of the tin-cans who helped attack the Earth and kill his family was behind the glass. He remembered how pleased he was when he found one wandering alone. He snuck up behind it and took out its eyestalk, before dodging its sporadic laser. He knocked off the lasers the pepper-pot possessed and dragged it back to a warehouse. He pulled off the armor and inside was a disgusting green alien with tentacles. It screamed for mercy, but it didn't show his family any mercy so why should he. It was the first alien he killed and after that it became an adrenaline rush. A need. Every alien must die.

* * *

The Doctor leaned his head against the back of the box, moaning. It was so hot and stuffy, he felt like he was suffocating. He hated being in tight spaces because then he couldn't move around and he liked moving around. He had been in the box for almost a whole day, maybe two. Yes, possibly two. He had lost track of time, but it felt like two days. He groaned, two more days to go. Breathing the same air and feeling stuffy from the heat. He had to give these people credit, they did know how to torture others. The Doctor's head slumped slightly and he slowly banged on the wall with his fist. He didn't know why he was banging on the wall, maybe he was already losing his mind. That would be a terrible loss. Where would he end up if that was the case? Oh, right the Underground. Locked up in a bloody cell, like a rabid dog. The Doctor sighed. He really hated being alone, his thoughts always ran down a more negative path nowadays. That's why he liked having company, it distracted him from the knowledge of how much his life sucked. Whoops, there he goes again, pessimistic thoughts. He should be given a dime for every time he thought negatively. He would be rich.

The Doctor turned his head slightly, when he heard the soft clomps of boots and the rustle of someone bending down next to his box. His ears perked, when he heard the lock unlatching. Visitors, already. He moved around, trying to make himself more comfortable, when the doors were thrown open and bright light attacked his eyes. The Doctor threw his hands up to block the sudden assault, when he smelled a familiar aroma. Food. Actual food. Not the sludge they claimed was food. He dropped his arms and the smiling face of Jake met his eyes.

"Hey there, Doc," He chirped. It was obvious he was trying to make the situation better. "How's it going?" The Doctor wasn't amused.

"I'm stuck in a box," he irritably stated, "What did you expect." Jake's smile dropped and he rubbed his neck embarrassed.

"Sorry," he meekly replied, "Was just trying to make the situation better, I guess." The Doctor glared at him, before shrugging.

"What's in the bag," the Doctor asked, "It smells like food and I am really hoping it is because I'm sick of sludge." The Doctor paused for a second. A quizzical expression graced his face. "Also, how did you get here. The surveillance cameras would of caught you sneaking in as well as the guards." Jake shrugged and pulled out a sandwich and a bag of chips from the bag and handed it over to the Doctor, before handing him a bottle of water. The Doctor took it greedily, tearing a piece of the sandwich off and shoving a handful of chips into his mouth. That answered his first question. He waited for Jake to answer the second.

"The guards were on a lunch break and I said I'd take charge. I also messed around with the surveillance cameras, blocking this moment out of view. The surveillance team won't realize what happened." The Doctor nodded his head, before taking a large gulp of water. He hadn't realized how hungry he was until he smelled the food. The Doctor gasped and wiped the crumbs from his mouth.

"You should have left," the Doctor stated, "I told you to leave and now you're going to get in trouble if they find you." Jake raised a quizzical eyebrow and shook his head.

"Doc, you never told me to leave," Jake said, "besides even if you did, I wouldn't. I have a mission, a duty, to complete."

The Doctor stared at Jake and shrugged. He handed the paper scraps back over to the young guard and leaned back. Hopefully, he could cover up the scent of food from the scientists and guards. He didn't feel like being beaten again or forced to tell who gave him the food in the first place. Not that he would ever tell. "Oh," he replied, "Sorry, I've been telling people to leave left and right." The Doctor paused for a second, his brain trying to remember the conversation. "Right, I said I'll help you get out. Which means you should of left during the battle, that was your ticket out." The Doctor glared at Jake. "And what do you mean duty. Duty to kill and torture aliens because that's not like you Jake. You were telling me how terrible your job is and how much you wanted to get out. So, don't tell me that you have a duty to the Underground..." The Doctor was about to continue his rant, but Jake threw a hand up.

"Doc, shut-up," he snapped. The Doctor shut his mouth with a dramatic click of the teeth. "It's complicated and I can't tell you anymore then this. But I promise you, I will find a way to get you out. You just have to trust me." The Doctor nodded his head, his eyes still searching Jake for answers. Jake glanced at his watch and stood up. "I have to go. People will start getting suspicious. Talk to you later." The Doctor waved his hand slightly as the door to his tiny prison was shut in his face. He was submerged in darkness once more. Alone with his thoughts.

* * *

**I hope you enjoyed that chapter and got some background information on the characters. The next chapter will be Ama and Donna's journey. Plus, Maybe a bit of what the aliens back at the warehouse are up too. Please keep reading and reviewing and tell me what you think. :)**


	34. Chapter 33

**Thanks for all the reviews. I hope you enjoy this next chapter it is centered around Donna, Ama, and the escaped aliens. Please review! I love reviews!**

Chapter 33

Donna weaved through the crowds with Ama close behind. With stealthy, slick fingers, Ama pickpocketed a man walking by. When she brought the money over, Donna wasn't too pleased with the stealing but knew they had to take immoral measures to save her best friend. And if pickpocketing a man was one step towards saving the Doctor, then so be it. They had jumped aboard a bus, heading for Cardiff. Their bus ride to Cardiff was estimated to be a couple hours or so, but they ran into some problems along the way.

Anti-alien protesters had delayed their arrival time from two hours to six hours or so. They had halted the bus and climbed aboard. Their goal was to convert people into believing that all aliens were animals and should be locked up. Donna had grabbed hold of Ama's hand, trying to comfort the young girl. Ama buried her head into her hoodie, hiding from the haters. She didn't need to deal with this after everything that happened to her.

As the hateful and racist words continued, Donna's cheeks burned with anger at the ignorance of these people and had protested against their words. The humans on the bus weren't too pleased about her standing up for aliens and had called her an alien-lover and some other derogatory words. She and Ama were kicked off the bus, with food and other objects being aggressively chucked at them. Donna had never felt so furious in her life. The pure hatred and cruelty humanity had shown towards aliens was too much and she only felt disappointment for her race.

Ama and her hitchhiked the rest of the way to Cardiff. Some people willingly gave them rides, while others drove past them, pretending they didn't exist. None of the humans, they got a ride with, realized that Ama was an alien. Donna learned later that Ama had put a psychic mirage over herself, making her appear like a human teenage girl. She had altered the minds of everyone who came into contact with her, making them believe the lie as well. Through each ride, the two travelers had endured alien-hate speeches and radio announcements on alien terrorist who were tried and executed that day. Ama wouldn't speak about it, no matter what questions Donna asked. If this was her future, Donna wanted to be as far away from Earth as possible. She planed on traveling with her Spaceman forever and she was going to make sure that happened. She didn't want to be apart of a world that hated differences. They had thanked the young man who dropped them off in Cardiff and begun their search.

For the past couple of days their search was unsuccessful and Donna was growing frustrated. It had taken them one and a half days to get to Cardiff, thanks to delays and people unwilling to give them rides. Overall, it had been around four and a half days since their escape and they weren't even close to finding this Captain Jack Harkness.

"So," Ama stated. Her eyes slowly scanning the area. "What does Jack look like?" It was hard looking for someone when you didn't even know what they looked like. She glanced over at Donna, who was glancing through a touchscreen computer phone book, hoping to locate the name. Ama took a large bite out of the hot dog she bought with the money she stole. She quickly wiped the crumbs away from her mouth, leaning against the bench. Her eyes flitted over to the protesters that marched on the other side. Each protester held an anti-alien sign. Some signs stated, 'an only good alien is a dead alien' or 'why don't you go back to where you came from' and other derogatory terms that Ama didn't feel like mentioning. She sighed. Why did humans have to be scared about differences? It only helped open up places like the Underground.

"Don't know," Donna replied, "I don't even know where this Torchwood place is. For all I know, it could have been moved. Which would be very unfortunate for us." Ama sighed, tossing the wrapper into the garbage can. She jumped up to her feet,stretching.

"The Doctor didn't tell you anything useful," She asked, she lifted a quizzical eyebrow and crossed her arms. Donna shook her head.

"Spaceman likes to be vague," She replied, "I should slap him for that. He should of just did one of his vulcan mind trick things he likes to do and given me the information, right there and then. It would of saved me the trouble."Donna grumbled irritably under her breath and Ama stepped over to Donna's side and glanced over he shoulder.

"We Don't know what Harkness looks like and we don't know where Torchwood is," Ama stated, "I'd say we're stuck and should pray for a miracle." Donna glanced over at Ama and rolled her eyes.

"A miracle would work wonders," Donna replied, "We've asked loads of people about Torchwood and no one has heard of it."

"Another secret agency base," Ama stated. She stroked her chin and crossed her purple eyes in contemplation. "What would he be doing. Undercover work or chasing down criminals. Because I think I've heard of Torchwood before." Ama glanced over at Donna. "My memory's a bit foggy considering I've been locked up for three years and have no idea about current events. But I believe my Patoi...or I mean father told me that Torchwood was Earth's protection agency against alien criminals. Something like that anyways." Donna nodded her head and shrugged.

"Knowing the Doctor," She replied, "His friend is probably the type who likes running. I say we look for somebody who is chasing down aliens..."

"Or smells like time travel," Ama suggested, "If he's the Doctor's friend, he probably traveled with him. Has the Doctor ever talked about Jack?" Donna shrugged.

"Maybe. He normally doesn't like dwelling on the past," Donna stated. She strode down the street, Ama close behind her. "He likes to keep his feelings to himself, which is very frustrating when you're trying to understand a situation. It's like pulling teeth with that man." Donna's eyes flitted over to another group of alien-hate activists and she scowled at them. "Oi!" she shouted, "You should be ashamed of yourselves, hating on aliens. They're people too you idiots!"

The protesters screamed at her in anger. One yelling out, "Why don't you marry one, Alien-lover!" They jeered at her and Ama and began throwing things at them.

"Maybe I will," Donna shouted, "It's better then marrying one of you lot!" The hissing and booing grew louder and more object flew their way. Donna grabbed Ama's hand and ran from the group of angry, hateful people. They ran around a corner, before slowing to a jog and then an easy stride.

"Was that really necessary," Ama asked, huffing from the sudden quick movement. Donna chuckled.

"No, But it made me feel better," Donna stated, "I really dislike haters. They always make me mad." Ama shrugged her shoulders. "You know the hate in Cardiff is a lot more extreme then in Birmingham. I wonder if its the location of where alien invasions were most often taken place."

"Don't know," she replied, "But if that is the case, better avoid London and New York." Ama laughed and Donna soon joined. They continued their tread down the streets, glancing through shop windows and pointing at the different dresses. If the situation they were in wasn't so serious and they weren't trying to save someone, it almost felt like two friends hanging out for the day.

"Stop!" Donna and Ama turned from the shop they were looking at, towards the male voice that just shouted. A Handsome man ran past the two women, his blue tailcoat flapping in the breeze, his teeth were gritted as he chased down a short, red alien with spikes. The alien seemed to run faster as the man caught up to it. Donna glanced at Ama, a smile lighting her face.

"I think that's our man," she stated, "Even dresses a bit like the Doctor. What is it with men and long coats." Ama shrugged her shoulders as a triumphant grin crossed her face. Donna quickly sprinted after the man and Ama soon followed suit.

The red alien squealed in fear, as the much taller man got closer. He glanced back and spotted two women chasing him as well and immediately sped up. He wasn't going to get caught anytime soon. He turned a corner, jumping down an open sewer hole. "Noooo!" the man shouted behind the red alien, "I can help you!" The man slid to his knees and glanced down the hole, but the alien had already disappeared, except for the quiet splashes of feet along the sewage floor. The man groaned, slamming his fist against the ground. He brushed a hand through his dark hair and closed his blue eyes. It was a lot simpler when he had his team. Except most of them were in New York now.

"Oi, You there sitting next to the sewer hole," A sharp familiar voice stated, "Are you Captain Jack Harkness." The man glanced up at the familiar ginger and a young alien standing next to her. His eyes widened and a grin crossed his face.

"Donna," he exclaimed, "Nice to see you again. How's the Doc and kids?" Donna's eyes widened in shock, before she crossed her arms and glared.

"What the hell are you talking about," Donna stated defensively, "and how do you know me? I've never met you in my life!" Jack's smile dropped and he awkwardly rubbed the back of his neck.

"I guess you're an earlier Donna then," he stated, "My mistake." He quickly got up and put on a charming smile. "Hello, Captain Jack Harkness at your service." He winked flirtatiously, before turning to Ama. "And who might you be, beautiful." Ama flirtatiously grinned back, holding out her hand. Jack shook it, grinning his charming smile. Donna rolled her eyes, crossing her arms.

"Amarzylda, from the planet Shianra," she replied,winking. "But you can call me Ama."

"Beautiful name for a beautiful lady," Jack responded, "Maybe we should catch a drink sometime. Get to know each other a little..."

"Oi! Captain flirts-a-lot," Donna interrupted, "Make a date later. The Doctor's in trouble and I've traveled all this way to find you." Donna crossed her arms. "Flirting can wait." Ama stepped away from Jack sheepishly, a slight blush tinting her blue skin. Jack stood up straight, all the playful flirting gone.

"What do you mean the Doc's in trouble," Jack asked, "What happened Donna?" Donna sighed, brushing a hand through her red hair.

"I mean exactly what I said," she responded, "Long story short, we were kidnapped in Cardiff and dragged off to some secret agency that experiments on aliens. The Doctor's still stuck down there and he told me to find you and Torchwood." Jack nodded his head, scratching the back of his neck.

"Alright," he responded. Donna could practically see his brain ticking with plans, "Where's the TARDIS?" Donna shrugged.

"Probably there too," Donna answered. "It was a hectic escape. Spaceman basically released every prisoner down there. Some wanted revenge, others just wanted to get away. The place wasn't successfully shut down. But almost every alien did escape."

Jack nodded his head, his blue eyes staring off into the distance. "We need to get back to the Torchwood base. Most of my team at the moment is in New York except for a few. I came back because somebody needed to keep an eye on the rift and I was the only one qualified." Donna nodded her head. "Lets get moving. It's getting late and the sooner we get the Doctor out the better."

* * *

The trio strode down the street, watching the people quickly walk past them and the cars drive by. Donna noticed Ama taking quick glances at the attractive Captain, before shyly turning her gaze away. Donna couldn't help the smirk that formed. She took a deep breath as they turned a corner.

"So, Jack," she stated, "Why were you chasing that alien? It didn't look like a monster to me." Jack couldn't help the smile that formed on his face. Ever since he first met her, Donna always stated what was on her mind and wanted answers for everything. He was truly happy for the Doc. He needed someone like Donna in his life, to keep him in check and out of trouble.

"He fell through the rift," Jack responded, "I couldn't leave him out there on his own. Earth is not a safe place for alien foreigners at the moment. I think I startled him." Donna snorted.

"You would've startled me too, sunshine," Donna replied, "Tall bloke like you chasing after me, I would've ran for the hills as well."Jack chuckled, his blue eyes sparkling with mirth. Ama smiled shyly, before quickly turning her gaze away from Jack.

"Yeah," Jack responded, "You know my job's a lot harder then it used to be. I used to just deal with aliens, now I have to deal with anti-alien activist and hope no one gets killed. Ever since people learned about the aliens among us, violence has escalated. People call it cleansing the Earth. Human's are developing organizations, like the one you and the Doctor got trapped in, looking for ways to rid the alien menace. It's like the whole Earth is following Torchwood one's moto, 'if it's alien it's ours.' Part of the reason why cloning and other technology is advancing so quickly."

"I'm sure the Doctor knew about this," Donna stated, "Why didn't he tell me. Well, he told me a bit about the cloning but that's it. We could have done something about it."

"He probably didn't want you to worry," Jack responded, "Since it's so close in your future."

"But before we were capture. I was walking around with him," Donna replied, "I didn't see any of this. We got an ice-cream and everyone was friendly." Jack shrugged.

"He most likely took you down to an area in Cardiff that is pro-aliens," Jack stated, "They are few, but certain neighborhoods and shopping centers don't mind extra-terrestrial lifeforms. They welcome them, even excepting new foods and cultures from their planets." Donna nodded her head at the explanation. She would need to bring it up with the Doctor though. He shouldn't feel the need to protect her from the evils of the universe. She quirked her head to the side and a cheeky smile appeared on her face.

"So Captain," she began, "Tell me a bit about yourself. I know you don't think the same as everyone else or you wouldn't of flirted with Ama here or chased down that red alien to help him." She quirked her brow, about to continue, But Jack interrupted with a playful, flirtatious smile.

"What can I say. I'm a 51st century man who likes everyone," he stated, winking. Donna rolled her eyes, knowing exactly what he meant. Donna elbowed him playfully in the arm and Jack beamed at her.

"51st century huh," Donna said, "How did you end up here?"

"Ex-time agent," he simply stated. He held up his wrist. A bulky watch sat on top. "This is a vortex manipulator. It can take me to any place or time. Very useful actually, except the Doc doesn't like it. Says, its primitive and dangerous." Donna laughed and shrugged her shoulders.

"Probably is," she retorted. "And I assume you know the Doctor pretty well." Jack laughed, shoving his hands into his coat pocket.

"You assumed correct," Jack replied, "I traveled with the Doctor in his earlier incarnation. He made me a better man. Sometimes I hate him for that." Donna nodded her head.

"Yeah," Donna stated, "Me too. He showed me the universe and now all I want to do is travel and help people. It's an adrenaline rush. The traveling, the running, the saving planets. It gets tiring but it's so thrilling and you can never get enough." Jack bobbed his head in agreement. "But he's my best friend and I would travel to the end of the universe with him."

"I have," Jack muttered. Donna raised a quizzical brow, crossing her arms. Jack coughed slightly, clearing his voice. "Traveled to the ends of the universe with him. It..it's a long story. Something for another time." Donna nodded her head, not pushing the matter any further.

"He's given me a better life. A life where I feel like I'm contributing something to the universe," She stated, Her eyes drifting off. "I promised him forever." Jack smiled, before glancing over at Ama. She had been quiet the whole trek back to the base.

"So," he asked Ama, "What's your life story. How did you meet our favorite Doctor and Donna." Ama blushed slightly from the attention and shrugged.

"At the same place where the Doctor is trapped now," she responded, "He rescued me and in return I want to help him."

"I'm sorry," Jack said solemnly. He didn't realize the young, Shian girl had been there. Ama shrugged.

"We can't change the past,"she replied. The trio continued their stride in a comfortable silence, until Jack turned into a building and the two women followed him in.

* * *

**I hope you enjoyed this chapter and I hope I got Jack somewhat right. I have never really written Jack before, so if he seemed ooc I'm sorry and I'll try better next time. I don't really watch Torchwood, so the only times I've seen Jack is in Doctor Who. Sorry to the people who wanted to see what the other aliens in the warehouse are up too, I just didn't know what to write, so maybe later chapters, I'll put a quick tid-bit in. At the moment you can safely assume they're just trying to survive and stay hidden. Maybe the next chapter. The next Chapter will again be a Jack, Ama, and Donna chapter and the Chapter following that will be about the Doctor. Please keep reviewing and tell me what you think. **


	35. Chapter 34

**Thanks for all the fantastic reviews! I'm glad I wrote Jack right. :) I created my own characters for Torchwood since it seems most of them have died in cannon Torchwood and this is in the future. Thanks again and here's the next chapter. I hope you enjoy. :)**

Chapter 34

A young, brunette woman with Asian features sat at a large computer, her eyes scanning over the information and pulling up readings on the rift activity. She heard the hissing as the doors to the elevator opened. Jack bounced out with two women behind him. A small smirk crossed her face before she turned back to the computer monitor.

"Looks like you brought a couple of _friends_ home," she stated. She swung around in her chair and raised a brow. A playful grin crossing her face, "Who're the lucky ladies." Jack beamed at her, giving her a playful seductive wink. He wrapped his arms around the two women's waist and grinned.

"These two lovely ladies, Becky, asked for help," Jack stated charmingly, "And I'm always here to be of assistance." Becky rested her head on her hand, a cheeky grin playing with her lips.

"In bed," she retorted playfully. Her eyebrow quirked, daring the captain to answer. Jack laughed.

"I wish," he responded. Becky heard the gasp from the red-head and couldn't help but chuckle when she saw her glaring at Jack and crossing her arms. The red-head soon broke out in a smile, shaking her head, her gaze turning to Becky.

"Hello Becky, I'm Donna Noble," the red-head stated. She held out her hand and Becky shook it vigorously. "Don't mind this bloke, his ego's too large for his own good," Donna said, leaning forward and winking. "I believe he would go into shock if somebody one day didn't fall for his flirtatious moves." Becky couldn't help the loud laugh that rolled up her throat. She slapped her knee, shaking her head playfully.

"Oh, Donna I like you." She turned to Jack, pointing over at Donna, before mouthing 'I like her a lot Jack.' She gave him a thumbs up, before turning to Ama. She could immediately tell the younger women was an alien. Her coloring basically gave it away. The young alien was glancing around the room, her eyes flitting to all the high-tech gizmos they had laying about. Becky's features immediately softened. The girl was terrified about being inside Torchwood and she was rubbing her hands nervously. Becky knew that something happened to the young girl and considering the world they were living in, it couldn't of been good. She got up and carefully walked over.

Donna moved over towards the computer console, glancing over the rift readings. This place was massive and like she had guessed underground. She turned her gaze over to Becky and a soft smile quirked her lips.

"Hey there," Becky said. The young alien girl glanced over at her, before shyly turning her gaze away and glancing over at Donna for reassurance. It surprised Donna how quickly Ama's personality changed. Before she was behaving playfully and was excited about the adventure. But as their journey continued, she grew more shy and quiet as if the toll of the last three years had suddenly just hit her. She opened up a bit with Jack, but that was short lived as she immediately clamped up and kept to herself. "Are you alright," Becky asked. The girl nodded her head, glancing around the room. She cringed slightly, as the place reminded her of the Underground. She was just happy it wasn't completely white.

"I just don't like places like this," Ama replied, "Sorry. They stress me out." Becky nodded her head and reached out to the alien girl.

"Don't worry. No one's going to hurt you down here," Becky stated, "I wouldn't allow it." Ama nodded her head, a thankful smile crossing her lips.

"Thanks," she whispered before copying the gesture Donna did. She held out her hand. "I'm Amarzylda by the way. But you can call me Ama." Becky smiled and took her hand, shaking it gently.

"Nice to meet you Ama," she responded, "I'm Rebecca Salt. But you can call me Becky or Becka. But I prefer Becky."

Jack smiled, before turning his gaze to the monitors. "So where's the rest of the gang, Becks?" Becky glanced over at Jack, before turning back to the Monitors.

"The rift was spitting out rubbish," she responded, "And since you weren't here, they went to deal with it." Jack nodded his head. "They'll probably be back soon. But..." She swung around, glancing at the computer monitor once more, taking quick peeks at Donna and Ama. "I want to know why they're here." Becky pointed over at the two women while at the same time watching the rift activity, "Because you said they needed help and we're always here to help." She swung back around, a kind smile on her face. She quirked an eyebrow at Donna and Ama. "What seems to be the problem?"

* * *

Donna told her story. From the capture, to being caught in the Underground for months, to finally escaping, and how the Doctor was still trapped down there. During her story, the rest of Torchwood's team ambled in. Dr. Kurt Parker, was the new Doctor of Torchwood who dealt with alien injuries from either hate-crimes, crash landings, or the normal injuries that the team seemed to get on the job. He was a Handsome man, with Mocha-colored skin and green eyes. His hair was a mess of corkscrew curls, and he had an attractive smile that showed a row of white teeth. Diane White was the next person to enter, her blonde bob and expressive blue eyes, gave her an image of a 1920's flapper, but there was a hidden strength about her. Donna had the feeling you wouldn't want to get on her bad side, it might get ugly. The last to pop in was Johnathan Wilkins or Johnny. His black hair was pulled back in a small ponytail and he had a small mustache and beard. His arms were covered in Tattoos and he looked like he belonged in a bikers-gang instead of Torchwood. The three newcomers sat down on the couch, listening to Donna's tale. Ama once in a while gave nervous glances at Johnny, who in turns glared back. He wasn't the friendly sort, but his heart meant well. Ama turned away, scooting closer to Donna. Crowds normally stressed her out, especially when it was people...humans she didn't know well.

Donna ended her tale and the group glanced among each other. They honestly looked upset after the story. Johnny folded his arms, glancing around his team.

"So," he stated, "When are we going to nail these suckers." Donna smiled at the response, glad to know that they wanted to help. Becky lept to her feet, running over to the computer monitor.

"It's weird that we didn't know this place existed," Becky stated, "I mean these sort of agencies pop up all over the place and teams like ours or UNIT normally are quite successful in shutting them down."

"A lot of aliens come to me, after one of those slaughter houses are shut down," Kurt said, "It makes me sick, how our world came to this." Diane patted him on the knee, understanding his feelings about the whole thing.

"If what you're saying is true," Becky continued, "Then this Underground has been around for a long time and UNIT might know about it. They've been shutting down these alien experiment establishments longer then we have." Becky quickly typed the area that Donna gave into the computer, seeing if she could spot any odd life signs or signatures that pointed to an evil underground agency.

"I just don't understand how Earth came to this," Donna stated, "I mean the time period I'm from, no one knows about aliens or if they saw something they write it off as a hoax. How come by 2015 Earth came to fear and hate alien life?"

"A lot of events happened in those years," Diane responded, "And it made people paranoid. The giant star in the sky, during Christmas, the Lazarus experiment, people exploding into fat babies, ATMOS."

"The Earth moving and the pepper pots," Johnny added.

"The 456 and the giant eyeball spaceship looking for agent zero," Kurt added.

"And anything else that falls through the rift," Jack concluded, "And all those events finally added up and people learned that aliens weren't quite the hoax they believed." The group nodded in agreement.

"And people freaked out," Johnny stated, "They begun believing all aliens must be evil because of the ones that attacked Earth."

"It started with a small group of hateful people," Kurt continued, "and that group protested which caused others to believe in what they said."

"And slowly the hate grew," Diane added, "where everyone hates that specific group but doesn't know why."

"That's when prejudice and discrimination begins," Donna concluded, "And that leads to places like concentration camps or in our case evil agencies that can continue to grow, thanks to people's hate."

"Hate spreads like a wildfire, it's love that is slow. It's a sick cycle," Ama muttered. She glanced around the room, at all the people who willingly put aside their work to help her and Donna. A small smile appeared. She was glad there was some good people left in the world. Diane smiled, nodding her head, and squeezed Ama's hand comfortingly.

"I remember reading about all of this in school," Jack stated, "when I was little. It was one of the lessons that we were taught in history. A reminder of not repeating the past." Jack dryly chuckled. "Funny thing is, I never expected to live through it." Donna nodded her head, patting Jack on the shoulder.

"No, no, no, no, no!" The Torchwood team, Donna, and Ama turned towards Becky, who was in the middle of yelling at the computer monitor. "You can't do this too me! You can't shut me out, you big useless piece of machinery!" Jack jumped up, jogging over to Becky's side. She was typing quickly, trying to pull up the site.

"What happened?" Jack asked, he watched as some alien virus ate up their computer.

"I found the Underground's database," she stated quickly, "And tried to break in. They had a massive code and I think I figured out half of it. But all of a sudden, this giant face appeared and ate up my computer, shutting me out. I now can't turn the computers back on." Jack nodded his head.

"Did you try reloading the Torchwood database or completely shutting it down and restarting," Donna asked.

"Or switching to our backup channel," Jack added. Becky glanced at him, mouth gaping.

"Duh," she stated, "I've tried everything. Somebody give me your laptop!" Kurt passed his laptop over and Becky immediately began opening it up and transferring wires and other software to the larger computer until the computer and the laptop were connected. "I'm going to try transferring the virus into the laptop," Becky continued. "Cross your fingers guys. Kurt I'll buy you a new laptop." There was a bit of hissing and some sparks, but the Torchwood computer flashed back on. The rift regulation monitor were back on once more. Kurt looked at his laptop that was completely fried and smoking. He unhooked the laptop and threw it away. "Sorry," Becky stated halfheartedly, to preoccupied with trying to find the site and location of the Underground again.

"It's fine," Kurt replied, "I'll just get a new one." Becky quickly nodded her head and Donna made her way over to the computer genius.

"Did you find anything," Donna asked, "Before you were rudely shut-down." Becky shook her head.

"Nada," she responded, "Well, I did find out the reason why we didn't know you or the Doctor were captured. Or Jack's vortex manipulator didn't detect the Doctor's presence on Earth."

"Why," Jack asked, bending in closer to the computers. The other four people in the room made their way over to Jack, Donna, and Becky. They leaned around Becky, waiting to hear the answer.

"Elbow room," Becky snapped sharply, shooing people back. She took a deep breath, before turning back to the computer, her fingers quickly typing on the keyboard. "There's an alien cloaking device over the underground headquarters. Making it impossible for people to spot anything going on. Plus, it is underneath an office building. More specifically a company that sells paper. So, completely nonthreatening. No one would ever suspect an evil alien-hating agency would be established there." Donna nodded her head, remembering seeing the sign. "Plus, as you witnessed what happened earlier, their security system around the whole building is ridiculously strong. I'm surprise you guys even broke out and now since they did have such a massive escape, they're probably making security triple the strength then it was before." She swiveled her chair quickly around, giving Jack a pointed look. "I don't mind impossible missions Jack, but in this case I think we'll need a bit of help." Jack nodded his head.

"Can we call in Martha and Micky Smith," Diane asked, "You said they were friends with the Doctor. They probably would be willing to help."

Jack shrugged. "I'm sure they would, Di, but right now they're in Zimbabwe, dealing with a terrorist attack. That area has so many wars between the locals and extra-terrestrials. Its ridiculous."

"UNIT!" Becky shouted, "Just call up UNIT. They most likely know about the Underground and are trying to find a way to shut it down."

"Plus, they're on good terms with the Doctor," Donna added, "I don't see why they wouldn't want to help."

Jack nodded his head, winking at the group. He pulled out a touchscreen cellphone and quickly dialed the number. The team, Donna, and Ama waited around the phone in anticipation. A click on the other end was heard as someone picked up.

Jack immediately went into business mode. "This is Captain Jack Harkness from Torchwood three in Cardiff. I need to talk to the brigadier in charge at the moment. We're dealing with a code three and assistance is required immediately." The team waited with bated breath as they waited for the answer.

"_Transfering you to Brigadier Jameson for immediate assistance under code 3, which deals with the Doctor in danger. Please wait for transfer."_ The group let out a thankful breath, before waiting for the Brigadier in charge to pick up.

"_Hello Captain,"_Jameson stated, _"You've alerted UNIT to a code 3. What seems to be the problem and how can we help?" _

A grin spread across Jack's face. "Hello Brigadier Jameson..."

* * *

"Roc! Roc!" Tak yelled, racing into the warehouse. Roc had organized the group of aliens, giving each alien a job to perform that day. Some of the more human looking aliens were set out to find food or get a job. While others, who didn't look human in any shape or form went out at night and collected things that the little colony might need. Some brought back electronics and those who were technological geniuses spent the day building holograms and other coverings for the aliens who stood out like a sore thumb. Overall, they were surviving and had made the warehouse homey. They had set up an area for sleeping and another place for hanging out and one of the aliens on a midnight stroll had found an electric stove sitting out on the street, waiting to be taken.

The smell of food wafted the large warehouse and aliens were sprawled allover the place, some finishing up their chores while others were relaxing and reading. Roc turned, hearing the young purple alien call his name. Tak was one of the last to escape, but overall had been the biggest help. Tak had basically become Roc's right hand man and willingly stood out on patrol and made sure chores got done. "What's wrong Tak?" Roc asked, catching the out of breath alien. Tak puffed out several more breathes and pointed towards the door.

"Men...men are out there," he wheezed, fingers shaking. Roc raised an eyebrow.

"Tak we live outside a city. I think if we see a few humans its not that big of a deal," Roc responded. Tak shook his head.

"No...no they weren't just people on the streets," Tak squeaked, "They had detectors and other searching contraptions. They were snooping around another warehouse a few blocks from ours. Roc, I think they're from the Underground." A collective gasp was heard from the aliens and panic immediately began to escalate. Chattering and small yelps of terror echoed throughout the warehouse and Roc attempted to calm everyone down.

"Everyone be quiet," Roc shouted. The aliens' chatter died down. "Just stay calm. We already know what to do in this scenario. We've practiced. If they come our way we'll hide or run."

"I say we fight," A small red alien with devil horn's shouted, his black eyes burning with anger. "I say give them what they're looking for! We are not cowards!"

"Yeah!" A group shouted in agreement.

"NO! If we fight, we are no better then them," Roc shouted, "And we risk losing someone. I personally want to go home. Donna promised once she finds help and rescues the Doctor, they'll take us home. Lets during this time avoid casualties. If they come, we run."

"But what about Donna," Tak asked, "If we leave, they won't be able to find us."

"Then we won't go far and we can easily contact Ama,"Roc reasoned, "Lets all keep a cool head."

"We should pack, just in case," A green alien with blue eyes stated, her tongue flicking out. "We'll need food and clothes." There was a murmur of agreement and Roc nodded his head.

"Fine," Rock agreed, "But lets wait. We don't want to act hasty and get caught. Donna is coming back with help she promised."

"But she's human," the slitheen hissed, "One of them."

"Yes, but she was also a captive alongside us," Roc countered, "And she organized our escape. I'm going to put my trust in her, like I did with the Doctor. I know Donna will help us." Roc glared at the slitheen, crossing his arms. "Who's with me." The alien's raised their hands, agreeing to the plan. Roc nodded his head. "Good. I need several people out there patrolling. If it is the Underground, I don't want any of us getting caught again." The others nodded their heads before a few exited the building, volunteering to patrol the areas. Roc glanced out the doorway. "Please hurry, Donna."

* * *

**I hope that chapter was satisfying and you liked my OC characters. Since this story is set in 2015, many of the original Torchwood characters are dead except for Gwen. So, I decided to create my own Torchwood team with Jack. Again I hope you enjoyed the chapter and you liked the characters. I wanted to thank thisdayandage for giving me the idea of the Underground staff looking for the aliens. Will the staff find them before Donna arrives? I do not know or I do know but I'm not telling you. The next chapter will be about the Doctor and the one following that will probably be meeting UNIT. Again thank you for the reviews and keep reviewing. **


	36. Chapter 35

**Thanks to everyone who reviewed the last chapter. It means a lot. :) So, here's the next chapter and I hope you enjoy it's all about the Doctor. Please review! I love reviews!**

Chapter 35

The alarms blared throughout the Underground. Soldiers quickly grabbed their weapons and ran out in search of the escaped prisoner. The clomps of boots on hard tiled floors echoed throughout the establishment and a young guard quickly hurried down the hall and towards the boss's office. The guard slammed the door open, with a heaving breath. Colonel Graham was already at the door at the first sound of the warning alarms.

"Sir..." The young guard wheezed, "Subject 13 has escaped again..." The guard pointed out towards the chaos outside as guards and scientists ran about looking for the runaway alien. "I don't know what it's doing, but it should know it's going to get caught and punished again." The Colonel slammed his gloved hand on the desk, quickly marching past the young guard. He stomped out into the hall, red lights flashed, turning the white hallways an eerie blood red.

"This is the second time in the last couple of days," the Colonel growled, "And the third escape overall. What are you planning freak?" He marched down the hallway, men and women racing about. Dr. Morley bumped into him and he grabbed her arm tightly, he glared menacingly. "Is the collar ready?"

Dr. Morley nodded her head. "Somewhat," she replied. The Colonel harrumphed, before turning away from the scientist.

"When we recatch subject 13, I want it collared," He shouted over the noise. He marched over to the weapons holding case, pulling out a tranquilizer, he stuck a pack of the darts into his pocket, placing three inside his gun. He marched out with a team of ten men behind him. Subject 13 wasn't going to make a fool out of him.

* * *

The Doctor had raced down the corridors for the second time in two days. They had released him from the box yesterday and he immediately escaped his cell after the guards left. The first escape he didn't get far, barely out the cell-block doors before he was shot down with the tranquilizers. He was given a warning but that only encouraged him to try again. This escape though, he had more luck. He couldn't pretend to be a scientists like his very first escape attempt, so he had to stick close to the walls and look for hiding places. He wasn't really trying to escape, if he was he'd be out of there in no time, but there was still a mystery to be solved and the Doctor could never resist a mystery. He swung around one of the corners, his feet softly padding along the hard white floors. The lights screamed and flashed their usual red. He had gotten used to that noise and it was the type of noise he wished to never hear again. Maybe he would try to leave. He could easily shut this place down from the outside. He skidded down another hallway and he noticed one of the exits he spotted in Norris's mind. How easy would it be to run up those stairs and never look back. But the sound of soldier's stomping feet echoed down the staircase, as a group of twenty men made an appearance. The Doctor ran the other way.

"All exits have been closed off," One of the soldiers hollered over the screaming alarms, "If it tries to escape we'll know." The Doctor sighed from the announcement. Great. Even if he wanted to escape, he didn't have a chance. He'd have to rewire everything and that could take too long and by that time, the guards would have already found him.

He ran over to the computer room, he had located on his first escape. By changing his voice and entering the passcode, he entered the room and quickly slid into a chair. Surprisingly, no one was guarding the room and he didn't have to send anybody off or knock them unconscious which was a bonus point. His fingers quickly typed in the code that he snatched from one of the technicians heads and he entered the Underground database.

"Let's take a look at security shall we," the Doctor muttered to himself. His fingers quickly ran along the keyboard as information flitted past his eyes. "Oooo...increase in security programs that's not good. Probably should try to shut those down. He quickly typed in a destructive code number and he heard all the emergency alarms slowly quieting. The information flitted across the screen and the Doctor watched intently. He weakened the traps and built in guns and lowered forcefields. "Lets cause everything to go a bit haywire," he stated. He typed in a code and everything seemed to go off at once. Hopefully if Donna was with Jack, they could easily locate his position in the Underground on the Torchwood's computers. He had figured out why Torchwood hadn't come to their rescue earlier The Underground was shielded under some type of cloaking device that was blocking their location. He believed with a little mayhem, they could easily find him. If they were looking. The weakened security would make their jobs a lot easier when they came to retrieve him.

The Doctor's tongue poked out of the side of his mouth as he glanced down at the chaos that was the bottom floor. Something caught the corner of the Doctor's eye and he immediately turned back to the screen. "What's this then," he asked. His eyes scanned the information and he scooted in closer. "Deadly pathogens from different planets...Man-made diseases... How to control a deadly pathogen?" The Doctor's eyebrows shot up to his hairline. "What are you planning Graham," he muttered. The Doctor clicked on the site and a screen full of numbers appeared. "A second code," he whispered, "You guys really don't want people seeing what you're doing. Don't you." The Doctor immediately began typing, trying to break the array of numbers, but each grouping he tried was denied.

_Bang! _The door to the computer room was slammed open and the Doctor turned around just in time for a giant gun to be shot off at him._ Swish! _A giant net unraveled in the air and slammed into the Doctor. The net quickly tied up around him and the Doctor struggled as he couldn't escape. He peaked through the holes of the net and shrieked as an electrical current spread through his body like a thousand sharp needles. The Doctor gritted his teeth, as a kick was placed firmly in his guts. The Doctor curled up, wrapping his arm around his stomach but the net didn't allow much movement.

"Well, well, well, look who we have here," A familiar voice stated, "I knew your curiosity couldn't resist the computer room." The Doctor glanced up at the cocky smile of Norris. Benson and Wells were behind him. "I think I deserve a promotion for my clever plan don't you agree." The Doctor screamed as more electricity coursed through his nerves, he screwed his eyes shut and gritted his teeth.

"You see," Norris continued, "I knew you were an arrogant sort and I thought 'what would subject 13 want to do if it escaped again?'" He slammed the cattle-prod against the Doctor's head, just for the hell of it. The Doctor squirmed, trying to escape the beating he was receiving. "And then it came to me. '_It _would want to head over to the computer room. Take a look around, mess with the security, and look at data before making its spectacular escape right under the humans noses'." Another swift kick was aimed for the Doctor's kidney's. The Doctor's eyes popped from the pain, back arching. "So I told the people who worked in this room to leave and waited for you to get comfortable before springing my trap. I deserve a grand reward for my ingenious plan." Norris slammed his iron-toed boot into the Doctor's knee. The Doctor heard a distinguish crack, as his knee gave out from the force. The Doctor wiggled in silent pain, but the net abstracted his movement.

"Congratulations," The Doctor squeaked out, pain evident in his voice. He breathed heavily, his eyes glassy. "You used your brain for once." Norris snarled and a boot connected with his nose. The Doctor moaned, squeezing his eyes shut.

Norris bent down, his breath tickling the Doctor's ears. "You know, I might not alert the Colonel right away. Me and the guys may decide to have a little fun with you before the Colonel comes. What do you say?" He glanced over at Benson and Wells and the two men nodded their agreement. The Doctor shook his head, eyes widening. A vicious smile spread across Norris's face. "Too bad. Three against one." He glared down at the Doctor and the Doctor squirmed slightly, wishing he could just disappear. "What game should we play first. I have a whole load of them. Benson? Wells?" The two men shrugged their shoulders and Norris grinned, pulling out his cattle prod. "Lets see how much electricity subject 13 can handle. I've never cranked the cattle-prod to it's full power before. Lets start on the lowest level shall we." Norris turned the dial, before slamming the prod into the Doctor's gut. The Doctor's eyes widened, knowing it could only get worse.

* * *

Colonel Graham was not pleased. He had been searching the whole agency for the past half hour and had no luck in finding the stupid alien. He knew it couldn't get out because the emergency doors had slammed shut, locking everyone in. If it did try to escape it would receive a powerful shock from the doors. But for twenty minutes or so, all the emergency and security settings had gone haywire and the Colonel was pretty sure he knew who did it. When the chaos ended, the Colonel ran up towards the control room, ten men behind him, collar in hand. Morley had handed him the collar, during the first five minutes of his search, quickly explaining how it worked. He wasn't going to allow subject 13 a chance to escape again.

He reached the top and screams of pain was heard from the room. A smile crossed his face. It seemed some of his men already found the little monster and was delivering its punishment. He halted the ten guards and leaned against the wall. The screams and begging growing more desperate as the punishment grew more intense. He was going to allow the punishment to continue until one of the men alerted him to subject 13's presence. The animal deserved it, if it was snooping around the control room. The screaming halted and loud desperate gasps for air took its place. He heard his comm. link crackle and he picked up.

"Yes, report," he growled out, watching the control room and the men moving around inside. He heard the loud whimpers of subject 13 on the other end. He couldn't help the cold smile that curled his lips. Served the animal right.

"_Sir, we found subject 13_," Benson said on the other end, _"He's in the control room. Do you want us to take him back to his cell, sir?"_

"No," the Colonel stated, "I'll come there. I'm not too far away at the moment." He heard a quick 'Yes,Sir' and the click of the comm. Link shutting down on the other end. He turned to his men and nodded his head in the control room's direction. "Lets go collect it, then," he sharply commanded.

He marched down the room, slamming the doors open, the ten soldiers close behind. Colonel Graham glanced around the room, spotting the three soldiers,Benson,Wells, and Norris. He knew them well from their reputation for tormenting the aliens. Norris was leaning against the computer console, a cocky grin on his face while Benson and Wells stood at attention. The Colonel glanced down at the alien gasping on the floor. Sweat and blood dripped down the alien's face and it was tangled in a giant net. It's eyes were squeezed shut and its arms circled around its stomach in agony.

It popped open one pained brown eye, its muscles spasming. Its eyes pleaded for mercy, but the Colonel didn't feel merciful today especially after it tried to fry their security system. He marched over and landed a swift kick to the aliens side, its eyes widening in pain and its mouth opening in a silent scream. Blood puddled around subject 13's body and its white skin was covered in dark, ugly bruises.

The Colonel squatted down next to the squirming alien, sneering in distaste. Why did he surround himself with these abominations, he never knew.

He grabbed the aliens chin tightly, forcing it to look up at him. Subject 13 tried to turn its head, but he squeezed his fingers tightly into subject 13's soft skin. "I'm disappointed in you subject 13," the Colonel growled, digging his fingernails into the alien's skin. Blood slowly dripped from the wound. "I thought we came to an understanding about trying to escape. But apparently you're too stupid to figure it out." He dug his fingers in deeper, eliciting a hiss from the creature. Blood dripped down his gloved hand. "So, now I'm forced to punish you and increase security." The Colonel yanked his fingers out of subject 13's chin and slowly begun untangling it from the net. "You see. I can't trust you to stay put. I gave you enough chances, but you continued to disobey me." He threw the net to the side, yanking the alien over to him. Subject 13 crumpled into his lap, its brown hair brushing his military uniform. Its freckles stood out against its pale skin and it breathed heavily obviously in pain. The Colonel pushed it off, forcing the alien to kneel in front of him as he stood to his feet.

"You see this," the Colonel stated. He held up the collar, placing it in the alien's line of sight. Subject 13's eyes widened, blood dripping from the corner of its mouth. "The scientists created this collar specifically for you. They predicted you would try to escape again so they created this little contraption to keep you in place." The Colonel smiled cruelly as he saw subject 13 shake his head and back away. "Grab it."

* * *

The Doctor tried to back away, but two guards tightly grabbed his arms, and forced him to stay still. He was still kneeling on the floor, his knees protesting against the discomfort of the floor. The guards dug their fingers tightly into his skin, bruising the soft flesh underneath their rough touch. He wanted to scream out and fight, but he was too tired. Norris and his gang had given him a beating that he didn't care to repeat. Electricity still coursed through his veins painfully because of it.

He felt cold metal clasp around his neck tightly and uncomfortably. He could still turn his head, but it was more of an struggle. The sharp edges dug into his neck, leaving raw marks. He already hated the collar, feeling like someone's tamed dog or something close to that. He already knew that the Underground looked at him as their property, but the collar somehow confirmed their beliefs. The Doctor felt many of his senses, including his time sense dull and he immediately felt panic run through his hearts. He realized he couldn't sense the psychic presence of anyone in the room or feel the strength in his arms and legs that enabled him to perform impossible feats that no human would ever be able to do. He felt extremely ordinary and that scared him. It scared him that the Underground created a collar that dulled his normal Time Lord powers, weakening him in the process. He glanced up at the Colonel in shock, the collar biting into his throat. He hated the collar, more then anything. It made him feel like he was below these humans. Nothing but a pet to be used and abused. The guards released his arms and he fell forward from the sudden lack of support. The Doctor crawled back to his hands and knees, he slowly reached for the collar but a powerful shock burned his fingers and he shook his hand in pain.

"No touching the collar," the Colonel stated, "Only me or one of the scientists can take it off. You'll be wearing that collar for now on. During your training and sessions with the scientists. During training, the Major will allow your abilities to awaken but the collar will stay on." The Colonel paused, watching the Doctor coldly as the information sunk in. "Through the collar, I can administer a powerful shock to your being when I witness you misbehaving. I can also type in a grid of how far I want you to go. If you go past that amount, the collar will either knock you unconscious or blow your head off." The Doctor gulped. "So, I suggest you don't try escaping again. I don't want to be forced to clean splattered brains off the wall." The Doctor nodded his head in agreement, bile rose up his throat at the sickening prospect of the collar. He was not pleased with the outcome of this situation. The Colonel pulled out a little remote, a wicked grin crossing his face. "Lets test out the collar. See if it works." The Colonel's thumb hit the button and the Doctor flew back to the ground as a strong electrical current hit him hard. The Doctor wriggled and squealed in pain as the electricity intensified before suddenly dieing down. The Doctor heaved heavily, trying to regain his equilibrium. "Good it works," the Colonel stated, pocketing the remote. The Doctor glared defiantly, furious about the shock collar and the whole situation he was in.

"Why don't you put me on a leash while you're at it," the Doctor snapped, he slowly crawled back to his hands and knees, blood dripping from his nose. He wiped the blood away and coughed painfully. A sharp kick hit him in the guts and the Doctor doubled over, his forehead touching the ground. Strong fingers grasped his hair, yanking his head violently back up.

"Don't tempt me," the Colonel grounded out, spittle smacked the Doctor's face. The Doctor clamped his mouth shut, not willing to test that theory. The collar was already humiliating enough without adding a leash. The Colonel released his hair and turned back to the soldiers. "Take subject 13 back to its cell and make sure it doesn't try escaping again. I'll go down there later and set the collar to how far subject 13 is allowed to move. I'll teach you how to use the collar so we don't mistakenly forget and blow its head off."

The soldiers grabbed the Doctor and yanked him up. They dragged him back down to his cell and tossed him in violently, the Doctor's face hit the ground hard and stars exploded behind his eyes. The familiar buzz of the forcefield turned back on and the Doctor rolled to his back, sighing deeply.

* * *

**I hope you enjoyed that chapter and please review. I decided to do one more Doctor chapter before the whole meeting with UNIT chapter. I hope you review and tell me what you think. :)**


	37. Chapter 36

**Thanks for the reviews everyone! I hope you enjoy this next chapter. It is the second confrontation between the Doctor and Dr. Morley. Please review! I love reviews!**

Chapter 36

The Doctor was rudely awakened from his somewhat pleasant slumber. His eyes popped open to the forcefield being lowered and he stretched his aching muscles as he was summoned to the front of his cell. His skin was still covered in the dark, purple bruises as the collar obstructed his healing factor. By now most of the bruises would be gone, but his wounds healed slowly thanks to the collar around his neck. He was yanked forward roughly as one of the two guards canceled out the movement restriction that the collar provided before roughly shoving him out into the hallway. His movements were sluggish and he felt like he was moving through a pool of jello with weights weighing him down.

The guards shoved him out the cell-block door and lead him down the hall, forcing him to turn a corner before standing outside a large door. The first guard knocked on the door and a muffled voice told them to come in. The guard opened the door and the other one grabbed the Doctor's arms tightly, pulling him into the room, he was shoved forward landing gracelessly on his knees.

The room was painted a warm red color and a couch was situated in the middle of the room with a chair across from it. A desk was at the far end with a potted plant next to it. Books were stored neatly on the shelves, put in alphabetical order. A brownish-red rug covered the ground and a closed door was on the opposite side of him. Overall, the room had a really homey feel to it. The Doctor caught Dr. Morley staring at him and he immediately climbed to his feet. Dr. Morley sat in the chair across from the couch, notepad in hand. The guards stood behind him, waiting for their orders. The Doctor itched around the uncomfortable collar, swaying back and forth since it was impossible for him to stay still for long periods of time.

"You can go," Dr Morley addressed the guards, she waved her hand to the door and the guards sauntered out, leaving the Doctor and Morley alone in the same room. Her gaze turned to the Doctor, who was standing awkwardly in the middle of the room, wringing his fingers. "Come here, Subject 13." The Doctor slowly moved over to the scientist, standing next to her, and waiting for her next order. "Sit down." The Doctor lowered himself to the ground, crossing his legs and sticking his hands in his lap like a schoolboy. Dr. Morley gave him a sharp look and he cringed slightly under the gaze expecting punishment. Instead she pointed to the couch. "I meant over there." The Doctor glanced over at the couch, an embarrassed blush tinting his cheeks as he steadily got back to his feet and shuffled over to the couch, landing heavily on the soft material. A sigh escaped his mouth as the couch was the first soft thing he had contact with for months and he sunk into the soft felt. His eyes drifted shut as he felt the comfort soothing his sore and pained muscles.

"Subject 13, please don't fall asleep. I have some questions I want to ask you," Dr. Morley stated. The Doctor's eyes popped open and he lazily watched Dr. Morley click open her pen and flip her notepad open.

"Why," The Doctor asked. He knew he wasn't expose to ask questions but curiosity always betrayed him. He felt himself grow more alert and he slowly lifted his head from the cushion.

* * *

Dr. Morley immediately noticed subject 13 growing more alert and its muscles tensed as if ready to run. She quickly jotted down the reaction and glanced over at the Time Lord's growing distress.

"Calm down Subject 13," she calmly stated, "Lay back and relax." That didn't calm the alien down instead the suggestion made it more antsy. It looked ready to jump and run for the nearest exit.

"Why," it demanded again, trepidation dripping from its words. "Why do you want me to calm down and relax. What are you planning?" Very interesting. Suspicion. She quickly wrote down the reaction. She didn't know if the personality trait was an original trait or one that grew because of its time in the Underground. She overlapped her legs and watched the alien's head swivel back and forth as it glanced around the room with a new found paranoia. It was as if subject 13 was waiting for someone to jump out and attack it.

"I just want to ask a few questions," she stated, "Don't worry I'm not going to harm you. If you misbehave, which I highly doubt it, I'll find another suitable punishment for you." Dr. Morley watched as the alien slowly settled down, its muscles relaxed as it took in her words. Its eyes still held the untrusting suspicion though and it followed her every moves, waiting for her to go against her word.

"Settle down," she hummed softly, trying to calm the creature. "relax." She watched as the creature slowly settled back into the couch and breathed deeply. She noticed it kept on scratching around the collar, attempting to fiddle with it before moving its hand away as its fingers were shocked painfully. She raised an eyebrow, watching the reaction before jotting down the information. She took a deep breath, preparing herself for the first question. She knew subject 13 could react in two ways. Either become extremely angry and violent or it would except its fate. If it was the earlier reaction, she would need to take precautions. She opposed violence but that didn't mean she stopped the guards from dishing out the needed discipline. She had a feeling it would be the later though since it hadn't lashed out yet.

"Do you know why you're wearing that collar," she asked conversationally, her eyes never trailing far from its facial expressions. Subject 13 subconsciously scratched around its collar, apparently the metal was irritating its skin. Subject 13 folded its hands into its lap, nodding its head. Its eyes glanced down at its fingers.

"Yes," it whispered, "For trying to escape again." It bit its lip in contemplation, trying to find the best way to word its next sentence. "Colonel Graham said I'm not to be trusted and I need the collar to make sure I stay where I'm at." She wrote down the answer, concluding that it knew why it was being punished. She wasn't surprised by the answer. She knew the creature was intelligent and understood what happened around it. It behaved a lot more meekly then her last confrontation with it. Possibly a newly developed personality trait, thanks to the recent conditioning. She hummed her understanding.

"But I don't agree with it," It stated firmly. Morley glanced up in shock from the sudden power in the alien's voice. Interesting, it seems to have two dominant personalities. The meek side that wanted to run and hide and the braver side that wanted to speak out and protest against its treatment.

"What don't you agree with," Dr. Morley asked curiously. She wanted to hear subject 13's explanation. It scratched at the collar uncertainly, groaning at the discomfort.

"Everything this place stands for," it responded. Dr. Morley raised an eyebrow, gesturing for it to continue. It squirmed slightly on the couch, not enjoying the attention. She wrote down 'doesn't like to be center of attention when speaking about personal matters.' She watched patiently as the alien tried to put its words together. It glanced around the room, focusing on the potted plant next to her desk.

"Subject 13 do you have a suitable explanation towards that comment," she asked. She gave the alien a pointed glare, tapping her pen against the pad of paper. She watched the alien fidget. It took a deep breath before its eyes met hers.

"What you do to aliens is wrong," it stated, "You hurt innocent people just because they are different from you and it disgust me. You treat us like animals, locking us up, and never letting us feel the brilliance of freedom again. Look what you've done to me. You've tortured me in the name of science, locked me away, trained me to be a killer, and when I try to escape this cruelty...you collar me like an animal with no care about how I feel or my aspirations in life." The alien laughed bitterly. "And you expect me not to run. To behave like a tamed dog and do your every bidding." Dr. Morley watched the alien grit its teeth in frustration. It was quite fascinating. There was no threats or vulgar comments, Subject 13 was just stating the facts as it saw them and addressing an injustice that it believed had occurred. It was truly fascinating to observe this creature's personality.

"And you feel like you're being denied these fundamental rights," Dr. Morley asked, "The rights that all people should have."

"Yes," subject 13 said exasperated, "Humans aren't the only ones with hopes and dreams. Many others out there have them too and you're denying them that opportunity when you lock them away."

"But you're just an alien," she stated.

"And you're just human," it snapped back, "See how it works." Dr. Morley pursed her lips, tapping the pen against her chin. She enjoyed having conversations with subject 13, they always turned intellectual and the discussions always led to the moral code of the universe. She would need to bring it in more often. It grows tiring dealing with angry, unreasonable aliens and subject 13 brought a nice change to the daily routine. Though seeing as many of the other aliens have escaped and subject 13 is one of the last they have until they find the runaways or acquire new recruits it seemed her intellectual and personality studies would mostly be based around subject 13. She did not mind this plan at all, though it would be nice to have one other alien around to see how its answers differed from subject 13's. She glanced over at the alien, leaning against the soft cushion of the couch awaiting the next question or for her answer. Dr. Morley didn't feel like answering its response so decided to switch to the next question she had in mind.

"You willingly helped the others escape but denied yourself the right for an easy disappearance," Dr Morley stated, "Why?" Subject 13 glanced over at her, shrugging.

"The others were there longer then I," it responded, "They deserved freedom. Me, not so much." Morley detected guilt when it spoke. It chewed on its lips, wringing its fingers all the signals pointed to a guilty person.

"Why don't you believe you deserve freedom," she asked, "When you specifically said that everyone deserves these rights." Subject 13 glanced down, shaking its head. Its jaw muscles had tightened and it heaved deeply, eyes glistening with unshed tears.

"Because I deserve this treatment," it stated, "I am guilty of so many crimes and I have ruined so many lives. Everything I touch dies in the end. I am death. I destroy planets and peoples goals, turning them into soldiers. I should be locked away. The universe is better off without me. I mess up and in return people I care about get hurt." Self-hate. That's what Morley noticed. It hated itself more then the Underground or the people working in it. Even questioning if it should try to escape its torment or stay. It honestly believed it deserved this treatment. Morley couldn't help but feel sorry for the alien. It was alone and she knew it. From her last conversation with subject 13, she knew something must have happened to its planet. Could it be suffering from post traumatic stress disorder or survivor's guilt? She sighed, knowing this question was going to be tough.

"What happened to your planet, subject 13," she asked. Its voice hitched with emotions and it...he let out an anguish cry and right then she knew what happened. There was nothing in the files she read that suggested he was alone, but the Colonel always hinted at it and the man, Anderson, mentioned it once around her and probably around the Colonel as well. But that comment finally hit home as she watched the alien's lip wobble with suppressed emotions that wanted to bubble over. Dr. Morley was not a coldhearted woman though sometimes she seemed to be. It was her scientific shield that protected her from the everyday life of the Underground. But her heart broke, listening to the hiccuped wails coming from subject 13. She couldn't imagine how he felt.

"Do you want to talk about it," she asked sincerely. He shook his head, curling up into himself attempting to hide from the world. "I think that's enough questions for today," she stated. She watched subject 13 itch his neck where the collar tightly clutched around his throat. She knew the collar must be uncomfortable, the collar was not yet finished. The collar did what it was expose to do and that was cancel out the Time Lord's powers and keep him tamed. But the collar still had a bit more development to go through and that would only appear in the second version.

"It looks like your collar is uncomfortable," she stated. Subject 13 nodded his head. "Don't worry the second version will come out soon and it will fuse more nicely to your skin. It's more flexible and won't obstruct your movement." Subject 13 didn't respond, instead curling into a fetal position. Hiccuped sobs wracked his body and she could hear the dry coughs of thirst coming from his throat.

She strode over to her desk and poured a cup of water for the alien. She walked back over, kneeling down next to him. "Come on. Sit up," she said, lifting the creature up slightly. Tear tracks ran down his cheeks and he quickly rubbed them away. Dr. Morley thumbed a tear away, a sad smile on her face. "Come on, sweetheart have a sip of water," she cooed, "And calm down." Subject 13 shook his head.

"Not allowed to," he said, "I'm in trouble." He let out a loud sniffle and the waterworks started once more. Dr. Morley pulled out a kleenex and wiped the tears from his face. He needed the comfort and as his psychiatrist she was willing to give it. He was still an alien, property of the Underground but even a pet needed reassurance once in a while.

"Let it be our little secret then," she said, "Come on just one sip your throat sounds sore." Subject 13 glanced at her suspiciously before taking the glass from her hand and taking a large gulp of water. "Not too much. I don't want you to get sick." She pulled the cup from his hand, making him take smaller sips. He really was thirsty. Subject 13 let out a satisfied gasp, wiping the water from his lips. He nodded his thanks to her.

Dr. Morley called in the guards and they marched the alien out of the room. She had learned a lot about the alien, just from their conversation and she hoped more sessions like this would be in the future. She wanted to understand the aliens different way of thinking and the best way of going about that was talking to him and treating him somewhat respectfully.

* * *

The Doctor was marched out of the room and down the hall. He had cleaned the tears away before the guards came but the memory of his planet still sat heavily in his hearts. He missed Gallifrey and the conversation he had with Dr. Morley had brought the painful memories back.

The war was set vividly in his mind. He could still hear the screams of his people at the first Dalek attack, watching the citadel crack and break as the monsters invaded the city. He could see the red grass burn under fiery flames and farmhouses exploding into debris and his people dieing unable to regenerate. The silver trees had burnt to the ground and more aliens, who were allied with the Daleks, destroying what used to be Gallifrey. He remembered traveling through the swampy marshlands of Skaro and other planets, sleeping under the harsh weather conditions with his troop and shooting at anything that moved. Overall, trying to stay alive. He remembered building time destroying weapons, which he felt quite guilty about, and everlasting prisons along with other genius Time Lords, desperate to win the war. But most of all he remembered his family. His family and friends burning or being shot down like animals. His wife had died in the first attack and he had told his children, his nieces and nephews, his cousins, anyone to run. But did they? He didn't know. He didn't know if they escaped, but one thing he did know he was alone and there was nothing he could change about it.

The Doctor was pulled to a halt and he realized he was nowhere near his cell. A sigh passed his lips. All he wanted to do was fall asleep and never awake again but apparently that was denied to him as well. The guard opened the door and pungent stench assaulted his nose. He couldn't control the hand that flew up and covered his nose. Even without his superior Time Lord sense of smell, the stench made his toes curl.

He was in a bathroom that had six stalls and four sinks, with a mirror over each, lining the walls. The tiled floor was grimy with mess and the sinks were dirty with rust and grease. He didn't even want to know what conditions the toilets were in. Colonel Graham stood in the middle of the bathroom, his arms behind his back and a bucket next to his feet. In the bucket was a sponge and something that looked suspiciously like a toothbrush. The Doctor sighed, already knowing what he was going to be forced to do.

"Subject 13," Colonel Graham growled, "I have decided on your punishment. Since beatings don't seem to have any affect on you, I have decided to punish you in a different way." He pulled out the toothbrush from the bucket and handed it over to the Doctor. "I want you to clean this bathroom, till it looks brand new. You will be using the toothbrush for the sinks and toilets and the sponge for the floors. I want you to scrub until every bit of grime, grease stain, rust stain, and any other stain has completely disappeared." The Colonel pointed over at the guard. "A guard will be watching you, making sure you're working your hardest. If he feels like you're being lazy, he will punish you as he see's fit. Do you understand?" The Doctor nodded his head, already growing use to the awful smell. He was not going to enjoy this.

"Good, get working. I want the sinks done first, then the toilets, afterwords the floor and stall doors, and lastly the mirrors. If you go out of that order, you will be punished. If you are slacking, you will be punished. If I come in here and I feel like the bathroom isn't to its cleanest, you will be punished. Understood?" The Doctor nodded his head and picked up the bucket, he walked over to the first sink and stuck the brush in the soapy water. He begun cleaning the first sink in the row of four. He heard the Colonel's clipped march exit the room as Major Johnson entered. Major Johnson stood next to the guard, arms crossed, watching the Doctor work. The Doctor's cheeks reddened in humiliation at the punishment that was bestowed upon him. He scrubbed the sink as hard as he could, hoping to get every grease stain off.

* * *

Hours had passed and the Doctor sluggishly moved to the last toilet. The toilets were smeared in brown waste and clogged with toilet paper and other things he did not care to mention. Each toilet proved to be a difficult task. He had to unclog them, which he was thankfully handed a plunger when he started and throw whatever crap he found down there away. His clothes were now covered in brownish grease and he smelled like sewage. He was not pleased with the outcome of his punishment.

He gasped in shock as the collar flung him backwards with a powerful shock, he clutched at his throat spasming, toilet sewage spilling allover the floor. Just as suddenly as the shock had started, it had ended and the Doctor found himself sprawled on the floor, gasping for air.

"No slowing down, freak," the guard stated. The Doctor glared at the guard, who was sat in a chair reading a magazine. He really hated his life right now. The Major had left after the first few hours,deciding to grab food, leaving the Doctor hungry and dirty. Stupid humans. The Doctor climbed back to his knees and began scrubbing the toilet with the toothbrush, grumbling ever so often at the unjust of the situation. It was the eighth time he was shocked off his feet and he believed the guard had a vendetta against him. The Doctor cringed as he pulled out a giant hairball from the toilet and quickly threw it into the bag, shaking his hand off in disgust.

It took him almost two hours to clean the last toilet, he scrubbed it clean and he was satisfied when he inspected it. Not one stain was on it. But now he had to clean the bathroom floors. He dumped the dirty water out and the guard handed him a new bucket with clean water in it. He immediately fell to his knees and began scrubbing the floor. The hard, rough floors dug into his already injured knee, causing pain to shoot up his leg, but the Doctor determinately ignored the sharp pain and continued cleaning the ground. He sloshed the sponge into the soapy water before slapping it to the floor as he slowly made his way through the room. He scrubbed as hard as he could, trying to get every last dirt stain he found off the floor. He heard the guard flipping through the magazine, paying him no mind. He quickly stopped, wiping the sweat from his brow, breathing heavily with exhaustion. Which earned him a shock from the collar and a sharp quip from the guard.

The Doctor washed around the toilets and under the sinks. He had been cleaning the floors for at least two hours, thanks to the guard's cruel move. The guard had gotten up and stretched before walking over the area the Doctor had already cleaned with dirty shoes. Mud once more was plastered to the ground and the Doctor almost loss his temper when the guard told him he missed a spot and cockily walked back to his seat, picking up a new magazine. The Doctor was forced to clean that area again. The Doctor glared at the guard. The Guard lazily flipped through the magazine, laughing once in a while at something funny he read. The Doctor grumbled, scrubbing the floor harder. Grease covered his face and his clothes were wet with soapy and toilet water. His knees were bleeding from kneeling on the hard ground for too long and his hands once in a while twitched from the after affects of being shocked. A wry smile crossed the Doctor's face and he began whistling the song 'Whistle While You Work' from the Disney film 'Snow White.' He continued whistling and scrubbing, letting his thoughts wander aimlessly. A powerful shock blew him off his feet and he found himself crumpled on the floor, gasping for air.

"No whistling," the guard stated, turning back to his magazine. The Doctor rolled back to his hands and knees and glared at the guard.

"What can I do then," he snapped back. He picked up the wet sponge once more, cleaning the floor with the soapy water.

"Clean,"was the guard's retort, flipping to the next page. The Doctor grumbled under his breath, giving the guard the death glare every few minutes.

He finished polishing the floors. The Doctor climbed to his feet and wiped his hands off on his pants. His hand swiped over his forehead, mopping off the sweat that spilled from his brow. He walked over to the first stall, bucket in hand and began cleaning each stall thoroughly. He made sure not to miss a spot as he scrubbed the door and the walls to the stalls clean. The bathroom was already surrounded in a soapy aroma instead of its original vulgar scent. The stalls were sticky and inappropriate comments covered the green stall walls. He scoured the writing, making sure there was no streaks left before washing down the dirt and grime. It took him half an hour for each but it soon was done and he walked over the wet floors carefully, taking care not to fall.

"Done yet," the guard asked indifferently, he peaked at the Doctor over his magazine. The Doctor shook his head.

"No, I just have the mirrors," he responded. He pulled out a soapy sponge and began cleaning the mirrors. He couldn't even see his reflection in the mirror as he cleaned it because it was coated in thick brown dirt. He put all his strength into cleaning the mirror and he soon spotted his reflection.

"Better hurry up," the guard stated, "Colonel Graham won't be pleased if the job is done incorrectly."

"What. Are you worried about me," the Doctor retorted sarcastically. He pushed the sponge down on the mirror and the grime finally budged, dripping away.

"No, I just don't care to watch you clean the next dirty room for another ten hours," the guard responded gruffly, "I prefer to just beat you for your disobedience. Takes less time." The Doctor scowled at the guard and quickly finished the first mirror before moving onto the next. Silence once again fell across the room and only the Doctor's vigorous scrubbing and the guard turning the pages of his magazine was heard.

The Doctor finished the last mirror just in time before Colonel Graham marched into the room. His eyes glanced at the Doctor before his lips curled in disgust. "You look filthy," he growled. He pushed the Doctor out of the way, who stumbled to the ground before steadily getting back to his feet. The Colonel glanced at the Doctor's handy work, slowly running a finger along every surface, checking for dirt. He flushed the toilets, listening to the swift swish, and nodded his head in approval. The Doctor stood there, waiting for acknowledgment as the Colonel made his rounds, inspecting the bathroom.

"Good, good at least you're useful for something," the Colonel sneered, "Maybe I'll put you on more cleaning duties. It seems to encourage you to put forth your full effort and we have plenty of rooms that need cleaning." The Colonel slid his finger along the top of the stall, pulling his finger back. A scowl curved his face. "What's this then?" He held out his finger towards the Doctor and the Doctor spotted a bit of dirt coloring the colonel's finger. The Doctor gulped in fear, quickly pulling out the sponge.

"I...I c-can c-clean that up," he stuttered out, he aimed for the stall but the Colonel pushed him back.

"No need to," the Colonel growled, wiping his finger on his pants. "I'll find a suitable punishment for you tomorrow." The Doctor quickly bobbed his head, dreading the thought of tomorrow. The Colonel turned to the guard and the guard stood at attention. "Take Subject 13 back to its cell and strip it of its clothes..." the Colonel ordered with a disgusted look on his face. "It's filthy." The Doctor lowered his head embarrassed as the Colonel turned out of the bathroom and the guard grabbed his arm, taking him back to his cell.

* * *

**Thank you for reviewing the last chapter. I love getting reviews and they only encourage me to update. Some of you may wonder why Morley started thinking of the Doctor as a he. She still views him as less then human, but he has proven himself to her that he is capable of higher thinking thus giving him a gender. I hope you review some more because the next chapter is with Donna, Ama, Torchwood, and UNIT including a quick glimpse of what's happening with the aliens. Please review and give me some feedback of what you thought. :)**


	38. Chapter 37

**Thanks for all the wonderful reviews! I'm glad you guys are enjoying the story. :) So, yes this chapter is about Torchwood, UNIT, Donna, and Ama and a bit at the end about the aliens. All my characters are original characters, except for Donna and Jack. Please review! I love reviews!:)**

Chapter 37

The Underground had proven to be a very secretive organization and from UNIT, Donna learned they never stayed in the same place for long. That's what made getting into the Underground so difficult. The last time, they had spotted it, it was in Germany before the whole organization completely disappeared. UNIT had lost an agent, who was undercover and couldn't gain contact again. They assumed the lone agent was dead, since he had been missing for at least four years.

The Underground apparently had been developed in 2009, a few months after the Earth moving event and had been growing ever since. The founder was, Colonel Martin Graham, who had lost his family in the first Dalek attack. He decided that all aliens were evil and needed to either be controlled or destroyed. He became one of the first activist to protest against alien lifeforms on Earth and more people soon joined him. But that wasn't enough for the Colonel, protesting did not suffice his goals. So he and a few shady businessmen decided to create the Underground. Rich, hateful men supported the organization, donating money to its cause while the Colonel went around hiring scientists and soldiers who had the same ambitions as himself. The organization grew and it was soon one of the largest and top leading experimentation labs in the world and many others tried to copy the agency, but UNIT had either shut them down or was close to shutting them down. But the problem with these type of places was that they always seemed to revive from the dead, making it completely impossible to absolutely destroy it.

"Ms. Noble," the UNIT officer asked, "Can you tell me one more time who alerted the Doctor and your presence to the Underground." Donna was frustrated, for the past two days she had been playing twenty questions with the UNIT officer and nothing seemed to be moving. After she and Becky figured out the location to the Underground, Jack had called up UNIT requesting help. They arrived a few hours after the call, but all searching seemed to come to a standstill. They began interrogating the Torchwood crew, herself, and Ama. Donna was worried about Ama's well being, since it seemed the girl wasn't doing to well and sunken into her protective shell even more. They had dragged her away and barraged her with questions about her time in the Underground. Which got Donna pretty angry, seeing as the wounds were still fresh and in the process of healing. She guessed UNIT was just desperate, since the last time they had contact with the Underground was at least a few years ago before they lost track and hearing that a massive escape took place was something new to them and their understanding of the Underground. Basically, no one ever escaped, if they did they were dead.

"I told you, you moron," Donna snapped back, "Some guy named Anderson. Complete idiot. Came in and gloated at me and Spaceman on our first day, saying how great he was. Is that enough information for you because I really prefer trying to get my best friend out." The Officer glanced at Donna indifferently, before turning to the notepad on the desk.

"What did Anderson look like," the Officer asked. Donna felt her blood boil and she slammed her fist on the table.

"I already bloody told you that," Donna shouted, "and I don't care to repeat myself. What is wrong with you people! One of your allies are being tortured in some evil agency and you're all sitting around drinking tea and repeating questions. Why don't you answer this! Why the hell aren't you breaking down the Underground walls right now?! You know where the place is!"

"We need to evaluate the situation," the officer stated, "It could take weeks."

"WEEKS!?" Donna shrieked, "We don't have a bloody week! I want the Doctor out of there and fast. I bet a slug could move faster then you lot. And you wonder why you can never catch these bastards! Well, here's your answer. If I lose Spaceman, you'll wish you never met me." Donna shoved a finger at the officer. "Got it bub!" The officer didn't even blink at the reaction, he just glanced down at the paper.

"Can you answer the question ma'am," the officer stated. Donna growled, collapsing back into the chair.

"Brown hair and green eyes," Donna stated, "And he looked like an idiot."

"Can you be more specific Ma'am," The officer asked. Donna's fingers curled into fist. Somebody was going to be slapped and it looked like the officer in front of her was going to be her next victim.

"How specific do you want me to be," she hissed irritably. The officer was about to answer when a tall, fit man with graying hair and a bushy mustache walked in.

"That's quite enough Reynolds," the man stated, "I think Ms. Noble has had enough of your interrogation methods. I'll talk to Ms. Noble for now on."

"Yes, Sir," the officer said. He picked up the notepad, leaving the office. The man turned to Donna Noble, who sat there glaring at him. The man put on a friendly smile.

"Hello Ms. Noble," the Man said, "I'm Brigadier Jameson. I believe we got off on the wrong foot."

"You think," Donna snapped, "I've been playing twenty questions for two days straight with that bozo and we haven't even gotten close to helping the Doctor. And don't call me Ms. Noble it makes me sound single, call me Donna."

"Alright Donna,"Jameson stated, "And I apologize about our processing being so slow. I personally prefer an unorthodox intervention. All the paperwork and asking questions takes too long." Donna nodded her head, already liking Brigadier Jameson.

"Thank you for seeing reason," Donna responded, "When did you fly in?"

"I beg your pardon," Jameson stated. Donna scoffed and rolled her eyes.

"Oh, don't be like that," she exclaimed, "You weren't here when whole bloody UNIT arrived, meaning you just arrived. Which thank God for your arrival, we weren't getting anywhere with the clown in charge." Jameson shook his head, folding his hands on the desk.

"You're quite correct Donna. I did just arrive this morning," he said, "But everyone was being questioned, so I just let myself in." Donna nodded her head, picking at her nails. "But I couldn't help but overhear you talking about a man named Anderson." Donna perked up at the mention of his name. Jameson slammed his black briefcase onto the table, opening it up and pulling out a folder. He flipped the folder open and pulled out a picture of the man Donna was talking about. "Is this the man." Donna took the picture from Jameson's hand and nodded her head enthusiastically.

"Yes, that's him," Donna stated, "Who is he?" Jameson took the photo, placing it back in the briefcase.

"Frank Anderson, UNIT officer, who protected files that needed to stay hidden,"Jameson responded, "He was a traitor to UNIT."

"Well, duh, that's obvious," Donna stated sarcastically, "How did you know which Anderson I was talking about it could have been any Anderson."

"Your description of the man matched his and he was the only one with access to the Doctor's files besides me and a few of the other higher ups," the Colonel stated, pulling out another file and slid it over to Donna. Donna grabbed it, opening the file. Her face paled when she saw the pictures. It was Anderson in a room, dead.

"He was found dead in his apartment a couple months ago," Jameson confirmed, "A bullet through his head. Apparently, his contact didn't want to strike a deal with him."

"He was offered two million dollars," Donna stated. Her gaze flitted to Jameson. "for the capture of the Doctor."

"That is probably why he was killed," Jameson said, "Graham never pays and he never lets people walk away alive from his organization. That's why it's completely impossible to find witnesses."

"That sucks," Donna muttered. She gave the file back to Jameson, crossing her arms.

"Yes, it does," Jameson responded, "I've been working this case for a long time now and I believe even if we shut the Underground down it will still survive in the memory of others. Places like this will never die." Donna nodded her head in agreement, before placing her forehead against the desk and brushing her tangled red hair back.

"I just want to get my best friend out," she stated, "I'm scared to see what condition he is in. I just want to make him better."

"I understand Donna and I'll do what I can to the best of my abilities," He said, "I promise you, I will get the Doctor out but I'm going to need your help in understanding the situation. Can you help me?" Donna nodded her head, whispering 'yes'. She was so tired, she hadn't slept a wink since the escape because of her stress and worries for the Doctor. She yawned deeply covering her mouth.

"You look exhausted," Jameson commented, "You should get some rest. You'll need to be focused tomorrow." Donna shook her head.

"I can't I need to find the Doctor," she stated drowsily. The sleepiness had finally hit her and she felt her head drooping with exhaustion.

"You won't be much help to him if you fall asleep on your feet," Jameson said, "Come on Donna lets get you to bed." Donna's head shot up at the mention of bed, she shook her head quickly.

"No, no, no not yet. I have one more question before I hit the sack," She exclaimed, "I just remembered it and seeing as you are a brigadier you might know the answer." Jameson settled back down in the chair, waiting for her to continue. Donna's eye were red with exhaustion but she wracked her brain for the needed question. It was about her she remembered that. She didn't realize how tired she was until now, but the question was important and needed to be answered.

"Ok, when I was in Colonel Graham's office being interrogated, he told me that all my records apparently disappeared after the earth moving event. He said I basically didn't exist. Do you know why." The desperation in her voice was quite clear, Donna Noble needed answers and she viewed Jameson as her last hope. Jameson sighed, knowing he shouldn't tell Donna, due to her being an earlier version of her older self, but if he went around the question carefully, he might be able to give her just a tidbit of her future without causing problems for future events or in his case past events.

"You told us to hide your files," Jameson stated, "Your future self." Donna raised an eyebrow, her mouth opening and closing like a fish, trying to form a question. The only word that came out was.

"Why," she asked. She ran her fingers through her red hair, her blue eyes focusing on the desk edge while she chewed on her lip.

"Because you didn't want your information to be held against you," Jameson stated, "You wanted to disappear like the Doctor. People ask to many questions it's easier not to exist."

"Was it important," she asked. Jameson could practically hear her brain ticking and putting the information together. He had met Donna Noble before, an older version of herself. He had gone with the previous Brigadier to collect Donna Noble's information before stopping off at her house. She had given them a reasonable explanation and knew it was good idea to hide. They had done something similar with Captain Jack Harkness, covered his footsteps or gave him false identity since people had spotted him all across time. It was difficult hiding the people that needed to disappear but it was worth it, until some greedy bastard like Anderson exposed someone under their protection.

"Yes, I'd say it was worth it," Jameson responded, I think you should go to bed Donna." Donna nodded her head and slowly stood to her feet, her mind racing with new information. She stumbled out the door, her head clouded with exhaustion and Brigadier Jameson kindly led her out the room and down the halls to the sleeping quarters.

* * *

"No, I won't stand for this," Jack shouted, slamming his fist against the wall. "This is absolutely ridiculous! I will not wait around any longer. We go in and get the Doctor out and that's final."

"And how do you propose we do that Mr. Harkness," A young female officer asked, her hair tied in a neat bun. "If you don't know, the Underground is completely impossible to get into unless you have an inside man."

"Then we go in bullets flying," Jack snapped back, "We take down their security, shoot down the leaders, and then blow the place sky high."

"Oh, of course it's that simple." Sarcasm dripped from the UNIT officers lips. Jack growled, slamming his fist against the wall one more time.

"I want my friend out of there," Jack growled, "God knows what their doing to him. I promised Donna I'd save him and you and your stupid rules and regulations are making me go against my word."

"I don't think you understand the way the Underground works," she stated, "These people are prepared for everything. They hide from the outside world and constantly move so no one can follow them. Having them so close is a miracle in itself. It's practically impossible to get your friend out and he got lucky releasing everyone to begin with."

"You know you're really something lady," Jack stated, a slight sneer curving his lips. He knew he was angry and he was venting all of his anger on the pretty officer but he didn't care. UNIT's process was moving at snails pace and he knew if he was to go in alone he could easily shut down that organization. But a more rational side to his brain kept telling him to listen to UNIT they knew what they were doing and had been dealing with this place far longer then himself. He took a deep breath through his nose and closed his eyes trying to keep calm.

"Jack, we'll get the Doctor out, I promise," Diane stated, her blue eyes sparkling with determination. She rubbed Jack's shoulders, trying to release the strain.

"Then why aren't we doing anything," Jack griped, "By now we would have the Doctor."

"We don't know that, Jack," Diane said, "I think we should trust UNIT. They know these people better then anyone."

"Huh, that's funny if they know them so well why haven't they shut the place down yet," Jack snapped back, "It's funny. My old team would of already had the Doctor out by now instead of sitting around listening to a bunch of soldiers." Diane backed away from Jack, a cold glare in her eyes.

"Jack that is not fair," Diane stated, "And you know it."

"If you knew the Doctor, you would care," Jack retorted. Diane glared and Kurt walked in at that moment, watching the two argue.

"I do care Jack,"She exclaimed, "I may be new to all of this but I do care about what's happening to that poor man and trust me, people will pay for their crimes." Jack glanced over at Kurt and the recently materialized Johnny, a sneer crossed his lips.

"Why aren't you guys looking! The Doctor is out there, afraid and probably thinking we abandoned him," Jack shouted. The two men jumped at the sudden angry immortal and Kurt carefully walked forward as if approaching a wild animal.

"Jack you need to calm down," Kurt said, "You're not helping him in anyway when you're angry. Sit back and relax. Take a breather."

"I can't," Jack stated. He slammed his fist against the wall before biting his knuckle. "These people won't do anything if I'm not here to supervise." Jack threw his head back, squeezing his eyes shut. "God, I wish Gwen was here. She'd know what to do. And Owen, Tosh, and Ianto they would all know what to do instead of standing around being useless." Diane smacked Jack in the arm, giving him a sharp glare.

"Stop moping and dwelling on the past," Diane said sharply, "I know you miss them but we can't bring them back. I can't imagine losing my teammates but I know this job is dangerous and it happens. I will do the best I can for my team." Jack nodded his head, mumbling 'sorry.' He glanced up before turning his gaze back to Diane, Kurt, and Johnny, who seemed particularly unfazed by the outburst.

"I'm sorry," Jack repeated, "I'm just under a lot of stress." He ran his fingers through his dark hair, leaning against the wall. He glanced down the hall, hearing soft whimpers. He glanced back at his team. "Where's Ama?" The three teammates glanced among each other, before shrugging.

"I think they sent her to interrogation," Johnny stated, "They wanted to squeeze some information out of her."

"They did what," Jack exclaimed, he felt the burning rage approaching again. "Get her out of there! She's not mentally stable enough to answer questions about her time in the Underground." Johnny nodded his head and ran out the door and down the hallway to where the interrogation was being held. Jack spun back around to face the officer, his lips curled in anger.

"What were you thinking sending her in for questioning," Jack shouted, "She just escaped the damn place and now you're drilling her with questions. How do you think that would help you." The officer marched over to Jack, getting into his face. Her eyes burned with rage at the accusation and she crossed her arms. Kurt and Diane stepped back, unwilling to get involved in a fight.

"Ama knows more information about the Underground then anyone else since she's been there for three years," the officer shouted, "If we want to get in, we'll need to know as much as we can about the place."

"Why,"Jack petulantly asked, "You could of asked Donna or something it didn't have to be Ama."

"Because we once infiltrated the Underground," she said, " almost shutting it down. But they caught whiff of us and immediately ran. We lost a man to them that day. He was undercover as a guard, learning everything he could. We lost connection and we can safely assume he is either dead or unable to escape." The officer quieted down, a sad smile on her face. "I miss him a lot." The rage in Jack's eyes had dissipated and his eyes grew more understanding and gentle. He understood what it was like losing a friend. He had lost a lot of friends in his long life.

"What was the agent's name," Jack asked. The lady officer was quite beautiful. She had auburn hair with bangs that curled at the side and light brown eyes. Her skin was fair with freckles dotting her nose. Jack took her hand and rubbed comforting circles on the top. She glared at him but didn't pull away instead standing up straighter.

"His name was agent Jake Simmonds," She responded, " and he was one of the best undercover agents in UNIT."

* * *

Roc's eyes popped open when he heard the quiet patter of footsteps outside. He turned his head, hearing men's voices. Roc gulped in fear, knowing exactly who it was. He crawled over to Tak, shaking him awake. Tak woke with a snort and glanced up at Roc.

"Wha?" he slurred tiredly, rubbing the sleep from his eyes.

"Tak, they're here," Roc whispered fear tinting his voice. "We've got to wake everyone up and send them to the escape exit." Tak nodded his head and quickly rolled out of bed and approached each alien individually, shaking them awake. Roc did the same, occasionally glancing out the window and making sure the soldiers didn't attack. He could feel the fear rolling off of everyone and he wasn't surprised. Some of them wanted to cry out and run, but someone always covered their mouths, keeping them silent. Roc led them to the exit, quickly directing them out.

_Bang! _The doors flew open and the shooting began. The aliens ran screaming in fear, trying to escape the flying bullets and tranquilizer darts. Many used their abilities, protecting the weaker aliens from the attack. The older ones helped the younger ones escape, before being shot down painfully. Other aliens tried to drag their fallen friends away from the massacre. Roc ran among the bloodshed and screaming as he helped aliens find the exit, but he knew many had already died. He didn't know why they were killing them, he assumed they would just be dragged back to the Underground to await further torment.

The men with the guns hooted and hollered, enjoying the fear they caused and Roc wondered if they should of left earlier. He turned into his rock monster form and swung his arm around, swiping the humans against the wall. A large crack was heard as their skulls broke against the wall.

Tak stood behind him, defending three injured aliens. He lifted his nose smelling smoke and the room grew hotter, as fire consumed the building.

"Everyone run!" Tak yelled, "They set the building on fire!" Screams of terror echoed off the fiery walls and aliens of all shapes and sizes ran for their lives. Roc picked up the three fallen aliens and Tak and charged out of the building. Large trucks and helicopters surrounded the area and men scoured the area. Roc ran with aliens in hand, looking for a safe haven or hiding place. He ran down the streets and jumped into an area thick with trees and kept running. He knew many of his friends were either dead or recaptured and that sickened him. He wanted to cry out with frustration, but knew if he did he would alert the Underground to his presence. He set the injured aliens and Tak to the ground and quickly transformed back to his normal size. There group had downgraded and he didn't know if anyone else escaped. He allowed the four younger aliens to sleep as he took first watch.

* * *

**I hope you enjoyed that chapter. The next chapter will be back in the Underground. I hope you enjoyed this chapter and please keep reading and reviewing. :) **


	39. Chapter 38

**Thank you for reviewing! I love when you guys review it makes me happy. :) So, here's the next chapter and I hope you enjoy. Please review some more and tell me what you think. :)**

Chapter 38

Jake Simmonds wandered down the Underground hallways with a lot on his mind. He had been an employee of the Underground for at least four years, but before that he was an undercover agent for UNIT. He had sacrificed himself for his team, deciding to go deeper into the Underground, becoming one of them. He had done many heinous deeds that he was not proud of, but in the name of justice it had to be done. He had separated himself from UNIT, never reconnecting. He needed them to believe he was dead, so he could put his full effort in cracking the Underground's plan. All he needed was enough qualified evidence to shut this evil place down, but that had proven to be a difficult task since there were no laws on earth that said you couldn't treat an alien poorly. He had to find something that endangered the human race and because the Underground was completely unknown to the majority of the population, not including criminals and traffickers it was basically impossible to bring the Underground to the observation of the public. Plus, adding their constant moving they could just move somewhere where no one knew about their existence.

Jake swiped his card before opening the door and turning a corner quickly. He did not look like his normal meek self or at least the personality he had given guard Jake Simmonds, but like somebody who had spent his life training as a spy. He swiftly turned a corner, giving a shy nod to a couple of the guards, before his eyes hardened once more. His boots softly clipped across the floor as he swung around another corner, doing a quick zig-zag. It was quite a surprise to him when he saw the Doctor for the first time. He had heard legends about the alien, but never expected to meet him in real life. Especially in a place like the Underground, but he couldn't let the Doctor know about his cover so he pretended to be the nervous guard that didn't know what he got himself into. It seemed to trick the Doctor just fine, but he had a strange feeling that the Doctor knew him from somewhere. He just didn't know where.

Jake marched through a door that lead through an alien cell-block. The Colonel's office was situated there and it was also the quickest route back to his room. He knew he had to contact UNIT again, but would they trust him after all these years? He wasn't actually going to contact UNIT until he found enough substantial evidence, but the discovery of the Doctor being captured and tortured ended that plan. He had hoped the Doctor would get everyone out, including himself but it seemed that didn't work out as planned either. He even tried to reroute the security, allowing all the prisoners a chance to find freedom which he found was a useless attempt. He had found out last night, that the Underground had found most of the aliens and had either killed them or brought the ones they captured back to the agency. Very few had escaped but the Underground had sent their trained alien assassins after the missing bunch. Another reason, why he had to contact UNIT. Plus what he had seen of the Doctor, the Time Lord wasn't doing too well. He wasn't able to heal his wounds thanks to the stupid collar around his neck and he looked quite weak, ready to fall apart at the seams. He knew it was time to let UNIT know that he still existed and needed help immediately. He wanted both the Doctor and the captured escapees out of there and the only way to do that was to blow his cover and call his team.

Jake quickly marched pass the Colonel's office when he skidded to a stop. He listened closely, hearing shouting and swearing from the room. Out of curiosity, Jake moved closer to the door, leaning his ear against it. He heard the Colonel and what sounded like another soldier shouting at each other.

"I DON'T CARE IF YOU THOUGHT IT IMPOSSIBLE," The Colonel shouted, "I WANTED THEM ALL RECAPTURED AND ALIVE. NOT ONLY A FEW ALIVE, MANY DEAD, AND THE OTHERS GONE, YOU IMBECILE!"

"SIR, IT WAS THE ONLY OPTION! THEY ATTACKED US AND WE HAD TO DEFEND OURSELVES," the soldier hollered back, trying to be heard. Suddenly it grew quiet and only heavy breathing was heard on the other side.

"Is that so," the Colonel whispered menacingly. Jake heard a quick 'yes,sir' from the soldier. "Well, then I believe you out stayed your welcome." And what Jake heard next was the most horrendous sound he had ever heard in his life. It sounded like bones cracking and a snarl from a wild animal. The soldier on the other hand screamed in fear, begging for his life, and asked 'what are you?" Before the squelching sound of someone being brutally ripped to shreds was heard. Jake stood there, mouth gaping in shock as the carnage ended. He heard a distinct cough and squishing of feet on blood before the squeak of someone sitting down on the chair. He heard what he assumed was the Colonel picking up a phone and the soft muffle of someone on the other end.

"Tell Major Johnson I want all the aliens we recaptured separate from subject 13," the Major ordered, "Subject 13 is more obedient when it believes it's alone. I feel like the presence of other extra-terrestrials would only encourage it to attempt escape again." There was another muffled reply from the other end before the phone clicked off. He heard the Colonel get up and walk about in his office.

"And now what should we do with you,"The Colonel stated.

Jake decided this was a good time to leave. Face paled with horror, he quickly ran down the isle, exiting the cell block and disappearing around the corner. He sprinted all the way to his room, ignoring the guards that waved at him. He knew he had dropped his character and that was dangerous, but he was in too much shock to notice. He slammed the door shut to his room and crawled under his bunk. His hand searched for the comm link he was looking for, before his fingers curled around something metal. He climbed out from underneath the bunk, leaning against the desk. Luckily his roommate wasn't there because what he was about to do was sure to get him into trouble. He turned the comm link on to UNIT'S channel. He glanced around the room once more, before hoping to gain contact.

"This is Agent Simmonds reporting to UNIT. I have information regarding your case on the Underground. I know it has been a long time but you need to trust me on this. The Doctor is a prisoner to the Underground and he's not doing too well. We need a rescue team immediately. I can give you the coordinates and security codes right now. But you need to hurry," Jake stated, he glanced around nervously before giving all the information he knew. "Did you get that." Silence on the other end. Jake squeezed his eyes shut, hoping upon hopes that UNIT would record this message and it would make it into the right hands. "I may not be alive when you get here. The Underground always spots a traitor. I'm lucky I've stayed alive this long. But please hurry up. There are people who need your help..."

"You're right no one likes a traitor," a snarly voice said behind him. Jake turned quickly around, his comm link still on. The comm link fell to the ground. The Colonel stalked closer to Jake and Jake couldn't help but back away slowly. It was like facing a wild animal on the hunt.

"How did you find me out," Jake asked bravely, his fingers twisted around a baton on the table. His heart raced in fear, but he kept his nerves steady.

"I smelled your scent lingering in the corridor," the Colonel growled. He sniffed the air before sighing pleasantly and quirking his head to the side."Ahhh, fear."

"Who are you," Jake asked back. He held the baton tightly in his clutch. The Colonel quirked his head as if evaluating his prey. He stepped closer to Jake, hot breath caressing Jake's face.

"A new race of humans," the Colonel snarled, before a heinous, animalistic growl exited his throat. He lept forward and Jake screamed in fear as the sunglasses were knocked off and the gloves broke with the pressure of something sharp protruding from the tips.

* * *

Since Brigadier Jameson's arrival, life had become quite busy in the Torchwood base. The UNIT officers were finally pulling their weight and looking for a way to get to the Doctor. Everyone had their jobs and each job was important for cracking the Underground security code.

Ama had stayed close to Donna after her whole interrogation experience. They apparently weren't very gentle and had treated her like a felonious criminal instead of an escape victim. She had cried in Donna's arms the night before wanting her Mum and Dad and finally giving Donna a glimpse of how young the girl actually was. She had shouted at the officers who had interrogated Ama and given a couple of them a sharp slap for their crude comments. Served them right. Jack also protected Ama. He had kept her out of sight from the UNIT officers, only allowing Jameson, who had proven to be quite gentle and good with abuse victims, to talk to her. Johnny surprisingly kept to Ama's side as well, unwilling to let another experience like the previous happen to her again. Johnny had never shown his soft side so publicly before, but with Ama it was different. He followed her around, behaving like her guardian angel and sneering at anyone who attempted to make her upset. Overall, Ama had grown to trust the Torchwood team.

The group was sitting in a dining room on a couch across from a UNIT officer who was trying to listen into Underground messages and phone calls but everything was distorted. Donna sighed, running her fingers motherly through Ama's hair. Ama had fallen asleep with tear tracks running down her face. Her head was in Donna's lap and she gave the soft snorts of sleep ever so often. Jack sat next to her, arms crossed. His foot tapped repetitively against the floor. He kept glancing about, looking ready to jump out of his seat and shout at people again. Captain Jack Harkness was definitely a man of action and didn't handle waiting around very well, even if the waiting around was important to finding a way to help the Doctor. Donna placed a gentle hand on Jack's leg and gave it a comforting squeeze. Jack glanced over at her and nodded.

"Everything is going to be ok," Donna said, "I want to get him out as badly as you do, but I know we have to be patient." Jack leaned back, sighing in exasperation.

"It's just taking too long," Jack responded, "I can't help but imagine the pain and fear he must be going through. Its been a week and nobodies shown up to rescue him. I bet he believes we've abandoned him." Jack leaned forward resting his head on his hands, his foot continued the rapid tapping. Donna patted Jack comfortingly. Jack glanced over, his eyes filled with desperation for action and justice.

"Jack, I understand," Donna stated, stroking Ama's hair and giving soft shushes as the girl's sleep became more restless. Ama whimpered in distress. Donna sighed. Was this what she was going to deal with when the Doctor got back? Maybe, she'd have him take her home and make him stay there. She could alert her Mother and Gramps to the events of the previous two and a half months and they could help heal him. Donna knew she was going to find a broken man in the place of the Doctor, it was inevitable. But she could be his friend and pull him out of the dumps, get him back on his feet. She didn't care if she never traveled again, she was going to be there for the Doctor and help him heal. The best place was probably on earth with familiar faces.

Jack glanced over at the whimpering girl, sadness weighing down on his heart. He couldn't imagine the horrors she witnessed, but then again he could. He had witnessed and been the victim of many heinous acts and because of his immortality, he never had a way to escape. He was going to be there for the Doctor, Donna, and Ama no matter what. Even if they choose to go back to the past and deal with the issues. He remembered that day when the Doctor and Donna arrived in the hub. The Doctor looked so broken and small and he couldn't help but wonder if that was the cause of this event. It probably was, Donna knew him then when he had no clue who she was. The mysteries of time travel. They had been staying with Donna's mother and gramps for a while, when Donna had suggested they visit Torchwood and the Doctor reluctantly agreed. After that life went spiraling out of control and the Doctor seemed to finally have loss it. Jack shook his head, exiting the terrible memory of trying to get the Doctor back on his feet without even knowing what occurred. He glanced over at Donna, who was softly comforting the distressed Ama.

"How's she doing," Jack asked, concern lacing his voice. Donna glanced up and shook her head.

"She's having a nightmare," Donna responded, "And I'm pretty sure I know of what." Jack nodded his head, anger flashing in his eyes. He never could believe how cruel people could be. These people...humans had abused a young girl so horribly that they probably destroyed her permanently, all because she wasn't human. Ama would never be able to go back to her normal self, thanks to the constant haunting memory of the Underground. Jack clenched his hand into a tight fist. He knew once he gained access into the Underground, people were going to die. He was going to make sure of it. Jack patted the whimpering girl on the shoulder comfortingly, letting her know that he was there. He wasn't going to allow anyone else to hurt her again.

Ama shot off of Donna's lap, purple eyes wide and startled. She turned to face the concern faces of Jack and Donna. Sweat dripped down her blue skin, as her eyes unclouded from the psychic alert she had just received. She pushed long, white hair out of her face and she glanced around the room in dazed silence. She felt like she was at the event. She felt the pain and fear from the others and Roc pleading everyone to stay calm before he finally had to run.

"Sweetheart are you alright," Donna asked, her hand gripping Ama's arm in concern. "It was just a nightmare." Jack moved over quietly, trying not to startle the distressed girl. This was no time for playful flirting and he recognized that look, seeing as he had met many psychics before, even spending a night with one. That was a pleasant memory, but right now his main concern was Ama.

"What did you see Ama," He asked softly but sternly. He wanted answers and he wasn't going to allow her to brush it off as none of their concerns.

Ama shook her head, curling into herself. Hot tears ran down her cheeks once more as a gasp of pain exited her mouth from the remainder of the vision. She wiped her tears away and Donna pulled her close, comforting the scared girl, and whispered comforting words in her ear. Jack kneeled down next to her, waiting for her to answer his question. Ama shook her head and put on her brave face. The others needed her help.

"Donna I'm ok," Ama stated, "I need to tell you something. Something important. It involves the others." Donna's face grew concern before a serious look graced her features.

"What happened?" She asked. Her hands clutched into fists as her worries expanded in her chest.

"The Underground found them," Ama answered, hurt and fear in her voice. She glanced off into the distance as if having another vision. "Last night. They attacked, killing many of the escapees and taking the others captive. Roc, Tak and three others escaped and another group went off somewhere else. But Donna the warehouse is gone. They're gone." Donna's face darkened in fury, her own version of the oncoming storm darkened her eyes, sending chills down Jack's spine. Donna had always been protective, but when the people she cared about were hurt or killed something dangerous always arrived, making her sometimes scarier then the Doctor himself.

"We need to go back," Donna stated icily, "This needs to end now." She got off the couch and marched over to the UNIT officer, who was busy trying to break the complex codes and find the Underground message channel. Donna stepped over, yanking the officer up and holding him by the collar of his uniform. Jack made his way over to the officer, he may not of known these aliens, but humans who went in and slaughtered a bunch of innocent people deserved to be destroyed. His eyes held the same fiery rage as Donna and the officer stiffened under the gaze of the two.

"We are going back to the warehouse," Donna stated steadily and coldly. Jack could sense the growing anger from Donna and knew if the officer said anything stupid, Jack may not be able to hold back the angry woman from ripping him to shreds. "We are going to find my friends and then me, Jack, and whoever else is willing to help is going to blow down the Underground doors and save the Doctor. Got it sunshine." The UNIT officer nodded his head. "Good." Donna released the officer and turned stiffly away.

"But Ma'am," The officer shouted, "The security is still up and we have no idea how this underground building is organized and protected. It's impossible to get in."

"We deal with the impossible on a daily basis,"Jack replied, "I think we can manage to break down a top secret organizations door."

"But it's highly unlikely," the officer stated, "There's regulations and a procedure." Donna turned quickly, fire in her eyes. She marched over to the guard and got into his face.

"Do you think I care!" She shouted, "I've wanted to get my friend out days ago, but you lot have been sitting around being useless. What the hell do you need to be able to ambush the Underground?!"

"Security codes and a whole lot of luck," the officer replied, standing his grounds. At that moment a miracle did happen. The recorder on the table began buzzing and a familiar voice spoke on the other end.

"_This is Agent Simmonds reporting to UNIT. I have information regarding your case on the Underground..." _The officer flew back to the seat, quickly trying to find the wavelength the feedback was reporting from.

"Go tell the others," He ordered, as he tried to gain contact with agent Simmonds. Donna stood there in shock as realization dawned on her. It was Jake. Guard Jake. The nice Guard who willingly helped them. He was a UNIT agent in disguise. That's why he was nervous about helping them. He didn't want to blow his cover.

Jack raced down the hallway, alerting both his team and UNIT to the news. Everyone ran back to the room, all gathering around the recording device. Jack sidled up next to Donna, leaning forward listening to the report. Everyone kept quiet as Jake relayed all the information he had on the Underground. The coordinates, the security codes, other valuable information they might need to get in and avoid being shot down, Back ways, everything. When he mentioned the Doctor, Donna's throat clenched in fear. She had expected the worse but to hear her spaceman not doing well sent fearful shivers down her spine. Suddenly another voice was heard behind him and Donna knew automatically who it was.

"_You're right no one likes a traitor," the Colonel said_. Everyone tensed with fear, eyes widening in shock. Donna covered her mouth, knowing what would happen next. There was more talking between the Colonel and Jake.

"_A new race of humans," the Colonel snarled._ Every one closed there eyes as they heard the heinous, animalistic snarl and the sound of a struggle. They heard Jake trying to fight the Colonel off, but Donna could tell the Colonel wasn't a man anymore. They listened to Jake being ripped to shreds and the screams of pain and terror cracking his throat. The struggle ended and only the heavy breathing on the other end was heard. The squelching of heavy feet on a bloody surface grew closer to the comm link as somebody picked it up.

"_That's a warning to you UNIT," The Colonel growled, "Stay out of the way." _There was a loud crunch and the comm link connection died, only static was heard on the other end. Everyone stood in silence around the recorder, none making a peep. Donna covered her mouth in shock, silent tears rolling down her cheeks. Jack pulled her close, a protective arm resting on her shoulders. Ama had moved over to the recorder and Johnny held her up, making sure she didn't collapse from sudden shock and pain. Kurt had wrapped an arm around Diane, both stood still, listening to the static echo throughout the room and Becky fingered a watch in her pocket absentmindedly, watching the wall straight ahead as her brain began piecing the information together. UNIT stood stiffly still unable to utter a word. They couldn't believe Simmonds was still alive, well used to be anyways.

"What the hell was that," Johnny asked, finally breaking the silence. Everyone glanced around and a sudden burst of action and chatter erupted as people began putting a plan together.

Donna jumped on the table, whistling loudly. The whole room quieted from the sudden noise. "Everyone listen to me," Donna shouted, "I have a plan." Everyone turned to the ginger woman, standing on the table. "We'll go to the warehouse first, rescue any aliens that escaped the Underground attack last night. Organize the dead, so we can send them back to their families. We'll organize an alpha team to enter the Underground, shutdown security, and rescue the Doctor and a beta team to back the alpha team up. We'll need a medical team outside waiting for the captives. Some may be injured and will need automatic medical attention. Knowing the Doctor, He probably already put the pieces to their plans together." She glanced over every man and woman in the room. "Who's with me?" Jack nodded his head.

"I'm up for the challenge," he responded. Others soon followed with their own agreements, nodding their heads or saluting.

"Alright then, lets get this show on the road," She shouted and immediately everyone went back to packing and loading up trucks outside. The whole Torchwood base was teaming with life and a sad smile settled on Donna's face. She walked over to the message feedback recorder, placing a hand softly on top. "Rest in peace my friend," She whispered. Jack watched the confrontation sadly. Donna's features contorted into a more serious and determined look. "Hang on Doctor, we're coming for you." She moved away from the recorder and stomped over to Jack and grabbed his hand. "Lets get moving. I want to be at that warehouse before sundown." Jack smiled at her bossiness and gave a mock salute.

"Yes, Ma'am," he stated, marching out through the door, tailcoat flying behind him. Donna smiled at the captain's cheekiness, before following after the quick paced captain.

* * *

Ryan Baskin gasped when he opened the utility closet and found two dead bodies ripped to shreds inside. Blood caked the walls and guts were tangled on the poles. A severed hand laid separate from its body as well as a foot. Ryan backed away a silent scream releasing from his throat. He had never seen something so disgusting and horrifying before. He immediately recognized the two men as Jake Simmonds and Sergeant Joshua Perkins, who had led the alien capture team last night. Ryan fumbled for his comm link.

"Somebody please report back," he begged into the comm link, he couldn't peel his eyes away from the carnage. "There's been a murder on the second floor. Please come." He waited for an answer but none came. "Jake Simmonds and Joshua Perkins have been murdered. This is Ryan Baskin speaking and requesting immediate back up." Ryan's face paled in disgust. He temporarily turned his gaze away and plugged his nose as the stench of death reached his nostrils. The comm link buzzed.

"_We're on our way," Somebody stated. _Ryan breathed a sigh of relief, moving away from the gore.

Ten minutes later soldiers and a medic team raced in and immediately began cleaning up the carnage. There was a lot of shocked gasps and horrified conversations when Major Johnson and Colonel Graham arrived on the scene.

"Who could of done this," Major Johnson muttered, moving over to the two dead bodies being zipped up. "Those were a couple of our best men." The Colonel shrugged, moving his sunglasses a bit.

"An alien," the Colonel responded, "They're evil creatures who enjoy killing for pleasure. My guess is subject 13. It has become quite angry recently. I wouldn't be surprised if it killed those two men." Major Johnson snorted at the thought of subject 13 killing brutally. He had to force the damn creature to pick up a weapon everyday at training.

"I highly doubt that," the Major stated, "Subject 13 doesn't kill willingly. Besides it can't escape."

"You never know," the Colonel stated, "It could of finally snapped and who says it can't slip its collar. It escaped its cell, releasing all those prisoners before." The Major nodded at the memory as he watched the medic team move the bags with the soldiers' pieces onto a gurney. He grimaced with disgust at the thought of one of those animals ripping those men to shreds.

"Don't know. It is possible, but I still have my doubts," the Major stated.

"I bet it did this," one of the soldiers snarled in reply, "I'm willing to punish Subject 13 for murdering Jake and Perkins. Jake was my friend." The soldier paused for a second, letting the information sink in. His lips curled in rage as he thought about subject 13 killing Jake. The creature was going to be punished."He didn't deserve to die. Me and a few of the others will take care of subject 13 tonight." The Major nodded his head indifferently.

"Just don't kill it," He responded. The soldiers smiled viciously, turning away from the Major and back to helping the Underground forensics team. The Major nodded at the Colonel, before tuning away from the crime scene.

"Oh, Major," the Colonel stated. He turned to the retreating Major and Johnson glanced back. "I think we may want to start organizing a new place to move to. I believe we've outstayed our welcome in Birmingham." The Major nodded his head, his arms crossed behind his back.

"I'll talk to our sponsors. See if they can set up a new place for us by tomorrow," He replied, "I'll alert the others to the move, get them to pack up valuables. We'll get a few crates set-up for the aliens and organize tranquilizers darts for the ride." The Colonel nodded his head, a sick smile on his face that even sent shivers down Johnson's spine.

"I want to be out of here as soon as possible," Was the Colonel's dismissive answer. "Also I want you to send out a few more assassins. I want them to find the last few runaways. Give them the orders to attack but not kill. You know how much they enjoy bloodshed." Johnson nodded his head and turned down the corridor. The Colonel stood there, supervising the clean-up job as they carted Perkins and Simmonds bodies away.

* * *

The Doctor was woken up from his restless slumber as six men entered his cell. Some held chains, while others held truncheons. Someone even held a cattle-prod that was sparking at the tips. The Doctor was yanked roughly off his bunk and thrown to the ground. He was confused and scared by the sudden attack and didn't know what he did to deserve it. He was hit heavily in the head by the truncheon, smacking his head against the wall. Blood seeped from the corner of his brow as he glanced up dazed and confused.

"What did I do," he asked. He couldn't hide the fear that tainted his voice. He was at the complete mercy of these men and from the looks of it they weren't going to be merciful. He was answered with another hit, this time to his thigh. He gasped out in pain as a sudden explosion of agony took over his left leg. He curled up in a protective ball, pressing close to the wall. He hated feeling weak, but at the moment he couldn't protect himself. From the beatings, humiliation, lack of food and water, the constant experiments and training, and the collar the Doctor didn't have the strength to fight back like he normally would. He was pathetic and he knew it. Something sharp hit him in the back and he yelped as fresh blood seeped down his swollen back.

"I hear you enjoy killing soldiers," the man holding the truncheon stated, "Simmonds was a good man and you killed him in cold blood."

The Doctor glanced up in shock. "What?" He asked confused. "Jake is dead?" He felt a deep sadness settle in his chest at the thought of another friend dead because of him. That was more painful then the beating he was about to receive. It probably was his fault anyways, even if he didn't give the killing blow. "I'm so sorry," He whispered. Stars burst behind his eyes as he was sharply smacked again.

"Don't you dare call him that freak," the man yelled, "You have no right you murderous son of a bitch. You're lucky the Underground wants you alive or I'd be tearing you from limb to limb just like you did to Jake and Perkins." The Doctor didn't answer. He didn't protest. He just allowed the beating to take place, knowing it would end soon.

* * *

**I hope you enjoyed that nice long chapter. I know it ended on a sad note, but the good news is UNIT has finally decided to take action! :) The next Chapter again is a mix between the Underground and Donna's journey. I hope you'll review and tell me what you think. Thank you again for reviewing last time. :)**


	40. Chapter 39

**Thanks for all the reviews! They make me very happy. Well, here's the next chapter. Tell me what you think.**

Chapter 39

"ROC! TAK! ANYONE!" Roc popped up, hearing Donna Noble calling for him. Tak slept close to his side and the other three aliens, who happened to be the slitheen, the graske, and the red alien with devil horns were sleeping in a tiny protective circle. They stirred as they heard the voice as well.

"ARE YOU GUYS OUT THERE!" A smile broke across Roc's face as he heard Ama's voice. The four lept up, looking over at Roc. Could the rescue party actually be here? Roc stood to his feet and cupped his mouth.

"DONNA! AMA! OVER HERE!" He shouted. The group glanced around the forest searching for their friends. He knew they were here, he just knew it.

"ALRIGHT WE'RE COMING!" Donna and Ama shouted at the same time. Roc couldn't help the grin that lightened his face. He was going home and this nightmare would only be a bad dream soon. He heard heavy footsteps trudging through the forest and Roc's smile began to dip. The footsteps stopped, but no one could see the familiar flash of ginger hair or the ever present psychic energy from Ama. Trepidation ran through the five. They immediately stepped into a circle, backs facing each other as they scanned the forest. They heard a rustle to one side and they turned their heads.

"WE'RE COMING!" Ama and Donna voice shouted again, "WHERE ARE YOU?!" This time Roc didn't answer back. Fear had overwhelmed his chest and his throat clenched in silence. "PLEASE COME OUT! WHERE ARE YOU?!" Ama and Donna's voice sounded like they were combined as one. They heard more rustling on the other side of the forest floor and Tak jumped as a white rabbit ran pass them.

"TAK! ROC! WHERE ARE YOU GUYS?! PLEASE COME OUT! WE HAVE HELP!" The voices shouted again. Roc felt Tak move closer to his side, the voices had grown nearer and the rustling of bushes more intense. A crow cawed nearby, circling the group before flying away. Roc didn't realize until now how quiet the forest had grown. None of the birds were chirping or the bees buzzing or the squirrels chattering. Everything was completely silent.

"There you are," Donna's voice stated. The bushes and trees were pushed back. "We knew you were there," Ama's voice completed.

Roc gulped. It's head was turned to the side as it walked out of the forest. Blood dripped from its teeth and rabbit fluff was plastered to its clothes. Its hair was thinning and sickly sharp teeth protruded from its gums. Its eyes were a pure obsidian black and it stalked crookedly towards them. Its head quirked to the other side a sick smile on its face. "There you are," it said in a combination of Ama and Donna's voice. "We've missed you." It walked towards the small group and Roc immediately stood in front of his friends. He had the best chance of winning against the alien assassin then the others did. It stopped, crouching low. Its hair dangling at its side. Its features were twisted and contorted from years of abuse and Roc could see the blood lust in its hateful eyes.

"Didn't you miss us," it said in a twisted voice of Donna's before switching to Ama's. "We've missed you. Come home now. Daddy misses you too." It chuckled in a disturbing combination of Donna and Ama, before pulling out a deadly knife. "Or we can kill you," it stated, "But Daddy wouldn't want that would he. He wants you alive." Roc transformed into his rock monster form and the assassin did a high-pitch giggle. "Oh, you're so silly." It moved closer to Roc, blood dripping from its mouth and its eyes crazed in desire for torture. "I know how to kill a rock monster. They have a couple weak points and then bye-bye to Roc." Roc cringed at the voice. It was strange hearing Donna and Ama say these things it made them sound demonic.

The slitheen gasped as two more assassins came out of the forest. They stalked closer to the five, teeth gnarly and skin icy. They looked practically dead like something from a horror film. Roc wouldn't be surprised if their limbs began falling off one by one. But that's what gave the assassins an eerie feeling. That struck fear in the hearts of people. They should be dead, but they couldn't die. They weren't allowed to until the Underground decided their fate. They were the aliens that had fallen. That gave themselves over to the Underground and didn't have the strength to fight back and stay strong. Some of the assassins didn't look so thrashed. Some of them looked hauntingly beautiful. The type of beauty that drew the innocent close and made them trust the monster, before they were brutally murdered. Those assassins were the scariest. They were like the mermaids from sea ship legends. The type that would lure and sing you to your watery grave. That tempted you with good fortune and prosperity before driving the knife into your trusting heart. They were the demons to the devil and the Underground was hell.

"Come back to us," It said in its corrupted Donna's voice, eyes widening with insanity. "You'll be happy and safe again." Roc shook his head, keeping his four friends safely behind him. A fourth assassin came out, one of haunting and tempting beauty. It glanced at Roc with promises of love and good fortune but deep down he knew what it wanted. Its hair was thick and it waved its hands in a welcoming gesture, blowing soft kisses and giggling with delight. It quirked its head to the side, smiling warmly.

"Come here my friends," it said hauntingly. Its voice was hollow, yet held a soft jingle to it. A welcoming jingle. One that made a person want to approach and trust it. Roc felt his feet move forward as if an invisible rope was dragging him closer. He struggled against the rope, but his feet wouldn't obey him. For some reason, deep down, he wanted to be with the beautiful assassin. It's high-pitch giggle, drew him out of the march to his death and that's when he heard the screams and fighting. His friends were fighting off the three dead-looking assassins as they lept on top of them, ripping into their skin with their deadly knives.

The slitheen threw one against the tree, before drawing out her sharp claws and running at the assassin. It flipped out of the way, landing gracefully on its feet behind the slitheen before plunging its knife into her shoulder. The slitheen screamed out, collapsing to the ground and like a pack of hungry hyenas, they pounced on her. Roc ran forward, swinging his rock solid arm, he flung them off the slitheen. He scooped her up in his strong arms just as an assassin jumped onto his back and climbed to his neck, stabbing him. Roc felt a shock of pain crawl up his spine and he grabbed the assassin flinging it against the tree. It slid down a twisted smile on its face.

"Please come back to us," it said in its demonic taunt, "I know you want to." Roc growled in denial. He ran forward, driving a hard fist in the assassin's gut. His fist went out the other end and the assassin's eyes widened in pain as blood dripped from its wound. A smile graced its face and its eyes for once were sane.

"Thank you," it moaned before collapsing dead. Roc withdrew his fist, stumbling back. He glanced at his now bloody hand in horror. He had never killed anyone willingly before and he felt sick to his stomach. He was broken out of his thoughts when he heard a soft enchanting singing and saw Tak walk pass him. He placed the slitheen safely up into a tree before turning around and holding Tak back. The hauntingly beautiful assassin continued its luring tune and Tak struggled to go over to it. The other two that were still alive were busy attacking the graske and the little red devil looking alien. The little escapees were busy trying to survive the vicious attacks, but their short legs didn't move fast enough. Roc knew they were going to lose. He had loss hope long ago when the four assassins arrived. No one ever escaped or survived an attack from the trained killers.

"Please Tak, don't listen to it," Roc begged, "Its getting inside your head you're stronger then this." Tak kept trying to follow the sweet musical voice. "Don't leave me Tak. Please break away from its pull." Roc glanced up to the singing assassin, its eyes were inviting but there was a hidden hatred beneath the welcoming smile. A killer's appetite. "Tak don't be tempted by its promises. Its lying!"

The graske had fallen and the other two pounced onto it like hungry wolves, teeth slashing in hunger and the fearful screams exited the graske's mouth as the little red alien tried to push the assassins off his friend. Roc couldn't decide who he should help. It was obvious that the graske was in danger, but if he let go of Tak, he would be taken by the other assassin in the woods. Roc for the first time felt conflicted and defeated. Either choice he chose would be devastating and people would die. He was a rock monster, he shouldn't feel this way. He closed his eyes and gritted his teeth.

"Somebody help! Please," he hollered. He lifted Tak into his arms, Tak's legs moving as if walking before Roc ran over and tried to pull the other assassins off of the graske. But they kept jumping back on top crazed with blood lust. Tak had began fighting him, wanting to be released. He was hitting and biting and Roc was worried he'd break his teeth or bones from the viciousness of his strikes.

_Bang! Bang! _One of the alien assassins fell to the ground dead, blood seeping from the two bullet size holes in its skull. Roc turned around to see a man marching out of the forest. His blue tailcoat flailing around his ankles and a gun in his hand. His blue eyes were sharp and focused as he watched the other assassin run at him. He shot another bullet but the alien lept out of the way, twirling, and landing steadily on its feet. The man kept on shooting at the alien, backing away slightly as the alien ran full speed at him, plowing into his gut. A stray bullet hit the other demonic alien in the forest. It screeched in surprise and pain, before it collapsed to the ground. Green blood oozing from the wound in its chest as its body twisted and contorted in pain before finally shriveling up and dieing.

Roc had pulled down the slitheen and gathered Tak, the graske, and the little red alien underneath him as the other bullets flew in his direction. His rock solid form protected the four as the bullets pattered against his skin. He heard the hungry and angry growls from the last assassin standing as it tore into the man that had helped them.

"Oh my God," Donna shouted as she stumbled into the opening with Ama close behind. She watched as the assassin dug its sharp teeth into Jack's throat, ripping out his jugular. Jack gave a gurgling gasp before the life left his eyes and the creature began digging his fangs and claws into him.

Ama boiled with rage lept forward, picked up the gun, and shot four bullets into the assassin. One bullet flew into the alien's arm, the second through the shoulder, the third into the chest, and the final blow straight through the head. The alien collapsed into a bloody heap. Ama dropped the gun in shock, her hand shaking with fear.

"Ama!Donna," the two women turned their gaze from the gore that covered the forest floor as they were pulled into a gigantic hug. Roc buried his face into the two womens' hair, smiling. "I knew you would come back!" The other four escapees surrounded them, leaping over and hugging the two women. Chatter and excitement erupted about help finally arriving. They told their stories and what had happened to the others but Donna only semi-listened to the tales.

Donna pulled away from the group and Ama followed. Roc, Tak, and the others watched the two move over to the dead body on the ground. They had forgotten about the man who saved their lives. The fear and excitement of the assassins arriving and then help appearing had blocked out the death of a hero. Donna kneeled down next to Jack, tears falling and splattering on the dead captain's face.

"I'm so sorry Jack," she choked out, "You saved their lives and in return lost yours." Ama's lips wobbled as she grabbed the dead captain's hand and glanced into his sightless eyes. The other five escapees stood around in silence, honoring the dead man. Donna let out a heartfelt sob, wiping her tears away. Too many of her friends were dead because of this place, but Donna knew she needed to stay strong and at the end she could mourn the dead.

There was a giant gasp and Jack shot up, his eyes blinking rapidly. Donna jumped back, screaming. She grabbed a stick, ready to beat the undead Jack over the head. Ama jumped away in shock, tears still trailing down her face. Jack rubbed the back of his neck as his throat and the other wounds he received healed right before their eyes. He squeezed his eyes shut and moaned. "Ouch." The other five had scattered and the four smaller aliens hid behind Roc, watching in shock as the man stood up and stretched his limbs. He glanced around in dazed silence.

"I'm telling you zombie," Donna hollered, holding the stick threateningly, "If you come after one of us and try to eat our brains, I will smack you a few." Jack glanced over at Donna, lifting an eyebrow.

"Donna," He asked. Donna shrieked, slamming her stick against Jack's head. Jack groaned clutching his injured skull. Donna swung the branch again but this time Jack was ready. He grabbed the branch, trying to yank it from Donna's grip. Donna screamed, struggling to pull the branch out of his grasp. She wasn't going to allow the undead Jack to eat her friends. Did the alien assassins have some type of virus that brought the dead back to life?

"Let go of it," She shouted, "Or I'll kill you! My brains are not a midday buffet and neither are theirs." She kicked out, hitting Jack with a calculated aimed kick. Jack doubled over, holding his crotch, and moaned in pain. "Yeah that's right you're still a bloke! Hurts doesn't it!" Donna waved the branch once more, pulling Ama behind her.

"Donna it's me," Jack stated, his face twisted in pain. He didn't need this at the moment. "and I am not a zombie." Donna hesitated for a minute, before holding the stick ready to strike again.

"How would I know that," she shouted, "It could be some type of trick." Ama tapped Donna on the shoulder, trying to gain her attention. "Not now Ama." She glared at Jack menacingly, though Jack could see the fear behind her eyes. Suddenly Donna dropped the stick, smacking herself in the head in realization. Ama couldn't help the smirk that crossed her face.

"Oh God. Zombies can't talk or feel pain. They're just the walking dead," she stated. She glanced over at Jack, who kneeled on the ground. "Jack is that really you?"

Jack nodded his head and squeaked a, "Yes." Donna kneeled down next to Jack as the other escapees surrounded the two.

"And you're not a zombie," she asked, trying to understand the situation. Jack shook his head. One part of him wanted to laugh at the situation, the other part wanted to curl up in pain. Donna really did kick hard. "Why then?" Jack glanced up, a bitter smile graced his features.

"I'm immortal," he stated, "I can't die." Donna nodded her head, taking the answer in stride. Why not? She traveled with a nine hundred year old alien. Donna shrugged.

"Ok," She stated, "That's a reasonable answer." Jack glanced at her in shock. In all his years he had never heard an answer quite like that before. Most people freaked out when he told them.

"And you're not freaked out or anything," he asked, just trying to wrap his head around her answer. Donna shook her head and scoffed.

"Look sunshine, I travel with a nine hundred year old man child," She explained, "And I travel through time and space. Immortality really isn't that shocking." Jack nodded his head, before climbing to his feet.

"Ok then," he stated, "Good to know." Ama ran forward, wrapping her arms around Jack's neck and gave him a quick kiss on the cheek. Giving him a sweet smile, she folded her hands behind her back.

"I didn't think you were a zombie," she stated, "Your life force was too alive to be an undead." Jack rolled his eyes.

"Thanks Ama, good to know," He responded. Roc pulled him into a hug, crushing Jack's body against his rock solid one.

"Thank you friend for your help," Roc stated, "I'm glad you're not dead." Jack nodded, patting the rock solid alien.

"Thanks," he muttered as he was dropped back to the ground. He put on a flirtatious smile and held out his hand to Roc. "Captain Jack Harkness and who might you be?"

"Jack," Donna growled, "Just don't, sunshine." Jack rubbed the back of his neck and smiled innocently.

"I was just saying hello," he responded. Donna crossed her arms, giving him a pointed glare.

"Just like you said hello to those UNIT officers right," She retorted.

"Sheesh, between you and the Doc I never get a break," He playfully complained, before giving a flirtatious wink at Ama, who in return blushed. Donna glared one last time before turning to the tiny group.

"Come on you lot," she exclaimed, "Lets get you back to the team." She waved her hand and began marching towards the camp grounds they set up. Jack shrugged his shoulders and followed Donna, with the other aliens following behind, chatting with each other.

"What about the assassins," Tak asked, he glanced concerned at the four dead aliens. Donna gazed over and sighed.

"We'll send a team to pick up their bodies and clean-up the mess," Donna stated, "And then we'll give them a proper burial. They deserve it." The group continued their tread in silence.

* * *

The Doctor hit the wall hard, before he lept back to his feet and danced around another powerful blow. The Major had him fighting robots again, since they were replaceable. The Doctor bent backwards avoiding a laser, that would have knocked him off his feet before he spun through the air, flipping over the robot, and kicking it in the jaw. The robot stumbled backwards, shaking its head before leaping forward and trying to grab the Doctor. The Doctor flipped away landing steadily on his feet before giving a deadly strike to the robot's arm. The arm popped off, wriggling on the floor.

After the beating he received last night, Major Johnson had switched off his collar, and allowed him to heal. His wounds were almost gone and his muscles didn't feel tight anymore which made training a lot easier today. Sadness still enveloped his hearts though as he thought of Jake's death. But knowing how Jake died only made him more determined to find out who really killed him. He already had one person in mind. The Doctor somersaulted as a heavy foot almost crushed his head, he lept back to his feet, knives in hand as he plunged the sharp blade into the robot's circuit. The robot sparked and stumbled about as its whole body shutdown from the electrical surge and the Doctor gave a victorious smile. It was nice having his abilities back, even if the collar was still around his neck.

The Doctor turned to face the Major, waiting for his next training session. But the Major wasn't paying attention to him instead he was speaking to a guard. The Doctor watched curiously, before enhancing his hearing. He frowned when he heard what they were speaking about.

"Is the equipment packed away," the Major asked. He glanced over noticing the Doctor watching them, he gave a threatening glare and the Doctor turned away, pretending to be busy.

"Yes, sir, I've got the carrier crates situated and ready for transport, all we need to do is pack up the aliens," the guard responded. The Doctor's ears perked curiously. What?

"Good, We're switching bases tomorrow. I want the move smooth with no obstacles in the way," the Major stated. He glanced over at the Doctor, waving the remote threateningly. The Doctor immediately began picking up the robot pieces and throwing them into the box. Worry clenched his throat at the thought of moving bases. If they moved him, Donna would never be able to find him and he'd be trapped there until they decide to kill him. The Doctor couldn't have that. He watched the guard retreat as a shock blew him off his feet. He laid on the floor, his body contorting and twisting in agony.

"No one likes rabbit ears," the Major sneered, "Don't listen into conversations that you're not apart of." The Doctor nodded his head rapidly, cringing slightly when the Major stepped closer to his side.

"Get up, you have one more training routine," the Major ordered, "Before you head over to Colonel Graham's office. The Colonel wants to speak to you." The Doctor nodded his head before stiffly standing to his feet and preparing himself for the next routine. He was dreading the thought of visiting the Colonel, but he knew he had no choice. He never had a choice. A blast shot past his head and he danced out of the way.

* * *

**Thanks for all the encouraging reviews. :) This next chapter will be another combination of both the Underground and Donna's journey. Please review some more and tell me what you think.**


	41. Chapter 40

**Thank you for all your reviews! They make me really happy! I hope you enjoy this next chapter and please tell me what you think! I love reading your comments.**

Chapter 40

The Doctor was yanked roughly down the hall, ever so often being kicked to the ground for not moving fast enough. It really wasn't his fault. The Major after training had switched his collar back on, making him feel weak at the knees. Normally, he had bounding energy that never seemed to end but because of the events of the Underground, his treatment, and the collar all that energy seemed to have disappeared. The Doctor was shoved to the floor once again with a hard kick to the guts for good measures. Honestly, if they wanted him to move faster, they should quit beating him on the march there. But the Doctor had a sickening feeling, they didn't care about punctuated time. They just wanted to torment him and make his life a living hell. It probably was part of the process of making an alien assassin. Beat the alien, train the alien, experiment on the alien, and make the alien feel completely at their mercy, it was a really awful check-off list. But what worried the Doctor the most was the moving bit he overheard from the Major and the guard's conversation. He couldn't afford moving because once that happened there would be no chance in rescue and Donna would be trapped in 2015 for the rest of her life. At least, hopefully, she would have Jack.

The Doctor stumbled to the floor again, hitting his knees against the hard ground. He stiffened as electricity coursed through his already abused body.

"Move faster and no thinking," the guard snarly ordered. He planted one more kick in the Doctor's gut before dragging the Doctor back to his feet and shoving him forward. The Doctor glared at the guard, a soft sneer forming at his lips. He really hated this place. There wasn't a lot of places that he despised, but this place was top of the list. He marched forward while the guard roughly prodded him in a certain direction. Well, they couldn't stop him from thinking that's for sure.

The Doctor had just finished his training session for the day and before that he had one on one time with Dr. Carter. The man was the definition of creepy and he prided himself in making the Doctor feel uncomfortable. The Doctor had spent three hours strapped to a metal table while Dr. Carter took blood samples and rambled to himself about a breeding program and how the Doctor would make a fine addition to it, considering his species was endangered and not a lot of people knew about their mating rituals. The whole monologue in the Doctor's opinion was quite disturbing and he didn't like the idea of a bunch of old men watching him do an act that was meant to be done in private. Carter had leaned in close, his lips spread apart in a excited manner as he checked the Doctor over for his weekly check-up. He really hated having Carter as a personal doctor but he really had no choice and Carter tend to enjoy rambling about his next ideas for an experiment with the Doctor in the room. The Doctor believed that Carter viewed him as some type of stupid animal that didn't understand English in any shape or form, which led to the Doctor listening to extremely uncomfortable topics that he preferred not take part in. Dr. Black had entered the room at that moment which made the Doctor blush from the embarrassing topic that Dr. Carter decided to grace his ears with. Dr. Black as always was indifferent to the situation and handed Carter the file that she held in her hand. A twisted grin broke across Carter's face as he read through the files, humming with delight. Apparently it was the go ahead for the program he wanted to start.

The Doctor shook himself out of that awful memory, his face paled with horror. He really hoped he'd get out of here soon. He really didn't want to be the father of a trained killer and as for himself, he didn't want to be a weapon either. It would of put a dent in his peaceful coexistence beliefs and other beliefs he had that didn't involve killing. The guard behind him rammed his truncheon painfully into his back as he began to slow down. The warning blow immediately sped up the Doctor's pace. He didn't feel like getting a beating right before his meeting with Colonel Graham. It would destroy his whole professional look. The guard pulled him to a stop and formally knocked on the door. A muffled 'come in' was heard on the other side and the guard opened up the door and pushed the Doctor through. The Doctor stumbled as his bare feet touched soft carpet.

He was led to a hard chair and pushed roughly into the seat as his hands were handcuffed to the desk and his feet to the chair. The Doctor glanced over at the stoned-face Colonel as the man in question flipped through a file, deliberately ignoring the Doctor's presence. The Doctor shrugged, his eyes scanning the somewhat decorative office and landing on the display case. An eyebrow rose in curiosity, before his brown orbs widened in fear. His hearts stood still for a moment as he gazed at the creature on display. His mouth gaped as the memory of a war that never happened hit him hard in the guts and the screams of destruction and fear throttled his ears and the horrifying electronic screams of 'exterminate' echoed through the room from the everlasting imprintment of the well known monsters of the universe. But why was one here? He had destroyed them during doomsday. they were sucked in the void, never to be seen again. But why was one on a display case? The Doctor's heart pounded in his ears and a lump formed in the back of his throat. His eyes never left the display case for it held a broken down Dalek. The eye stalk was bent at an awkward angle and the plunger and laser was somewhat cracked.

"Impressed," the Colonel asked, marching over towards the Doctor and glancing admiringly at his trophy, "First alien I killed." He leaned back against his desk, watching the Doctor's horrified gaze."Grabbed the hellish pepper-pot and tortured it to death." The Doctor's eyes shot over to the Colonel, who had a satisfied smile on his lips. A shiver ran up the Doctor's spine as he scrutinized the Colonel. There was something wrong with him and it wasn't the hateful darkness that enveloped his mind. The Colonel glanced over at the Time Lord, his black glasses catching the Doctor's reflection. He waited for an answer. The Doctor cleared his throat, organizing his next thought. It would be wise not to anger the unpredictable Colonel.

"Yes," he replied, "Quite impressive. It is difficult to kill a dalek, especially for a human." The Doctor cringed as the last part released from his mouth. Damn. That was a bad thing to say. A very bad thing. He glanced up nervously at the Colonel to catch his reaction and he could automatically tell he was in deep trouble. He gulped nervously and laughed. "Sorry for being rude?" The Colonel grabbed his hair, slamming his head against the table. Stars exploded behind his eyes and the Doctor gave a pain filled moan. The Colonel lowered his head and whispered into the dazed Time Lord's ear.

"I'd watch your mouth if I were you," he snarled. The only thought that passed through the Doctor's mind was 'since when did the Colonel get so strong and why did he feel something sharp poking into his scalp?' The Doctor nodded, blood dribbling from his nose. The Colonel released his hair and the Doctor lifted his head, his cheek already bruising from impact. The Colonel crossed his arms, staring at the dalek in the case. The Doctor sniffed, trying to stop the nosebleed without the use of his hand. He couldn't help but take suspicious glances over at the Colonel. He just felt wrong and the Doctor wanted answers.

"I killed that creature with my bare hands and a large rock," the Colonel continued. The Doctor could sense a hint of pride in his voice as Graham told his story. The Doctor was sure it was an intimidation technique and the Colonel wanted him to cower in fear and immediate submission. "I smashed the creatures eye stalk with a rock as it wandered alone." The Colonel smiled at the memory. "It shot at me blindly, but that gave me an advantage. I snuck up behind it as its deadly laser shot sporadically and it shouted 'exterminate.'"

The Doctor cringed at the word. He was very accustomed to that word and it was a word he wished to never hear again. "I took out its lasers and wrapped a rope around its metal body, dragging it back to a warehouse, where I proceeded to open it up as it screamed in pain and fear. The sound was glorious. The begging for mercy, the distress screams of agony and when I pulled the creature out, I laughed. It looked like a green squid. How could something that small cause so much fear? So, I killed it, slowly and painfully to let it know what the human race was capable of. What I am capable of and it felt good."

The Colonel turned his gaze over to the Doctor, a cruel smile on his lips. "You see I can do whatever I want to you. You're just an alien and no one cares about what happens to an alien. I could shoot you and no one would bat an eye. You're nothing but a tool to be used and destroyed when you outlive your usefulness. That dalek over there." The Colonel pointed at the dalek in the display case. "I killed it and people walked by, hearing its screams for mercy but they never came to its aid. I've done that to many other aliens before and no one ever cared because your kind is subhuman filth. Crap on the bottom of someones shoe." The Doctor turned away from the Colonel, wanting to block out the hateful words.

"It's difficult to kill a dalek," the Doctor said, "Normally they travel in groups, so why was this one alone. Even a lone dalek is difficult to destroy. It must have been injured. It had to be. Human or not, it's difficult to destroy a dalek without a tool of some sort to do so." The Colonel stepped forward, grabbing the Doctor's chin, and forced him to meet his eyes. His hot breath brushed the Doctor's bloody nose and the Doctor raised his head high, not willing to show the intimidation he felt. Yes, he did fear the Colonel. The man was unpredictable and he had a sick feeling that Graham was the one who killed the two soldiers. It was just the feeling he got around Graham that blared a danger warning sign in his head. He could sense it, Time Lord abilities or not.

"You're trying to change the subject," the Colonel growled,"You're in denial and don't want to believe what I am telling you." The Doctor shook his head but the Colonel's sharp fingers clutched harder. The Colonel spoke to him as if he were a disobedient child who didn't want to listen to the rules. A cruel, icy smirk curved the Colonel's lips. "Tell me this Subject 13 why hasn't your little ginger friend come back for you yet. She promised you didn't she," the Colonel asked. The Doctor nodded his head, his eyes never leaving the Colonel's. "You'd think that she'd be back by now, freeing you. How hard is it anyways. You got everyone else out, but why isn't anyone helping you?" The Doctor glanced down at his chained hands, puzzling with the question. Why wasn't Donna back yet? She should have been, but she wasn't. Why?

"She's just running a bit late," the Doctor stated, "She promised me..." The Colonel slammed his fist on the table and the table cracked from the pressure. The Doctor's eyebrows shot up to his hairline.

"NO!" The Colonel growled, "She abandoned you! As soon as she escaped she didn't care what happened to you because you're just an alien. Why would a human want to be around an alien?!" The Doctor shook his head in denial, watching the Colonel's face redden in anger. Colonel Graham itched at his skin irritably and the Doctor could see chunks of dead skin piling on top of the table. He blinked a few times before turning his gaze back to the Colonel's.

"That's not true," the Doctor replied, "I know its not. Donna wouldn't do that..." A fist connected with his jaw, cutting off what he was about to say. He gasped as his jaw throbbed from the sudden unexpected punch. The Colonel grabbed the collar of his shirt and yanked him off the chair, bringing him close to his face.

"Then why hasn't she come back for you or found a friend who could get you out, huh," the Colonel growled, "If she cared about you, you would have been out of here in no time. But isn't it obvious? She doesn't give a damn about a grimy, little alien." The Doctor's jaw tightened in anger at the words. Half of him didn't want to believe it, but the other half kept screaming at him, telling him it was all true, Donna abandoned him. Left him at the mercy of these psychopaths. That screaming voice grew louder and the Doctor couldn't help but listen to it. It told him that if Jack was coming he would've been here by now and other nasty things that he wished weren't true. The Doctor squeezed his eyes shut as the bombarding of different voices intensified. He could feel the darkness closing in and he fought it off, but without a friend or someone he cared about nearby the darkness was swallowing him whole. He screamed as the noises grew louder. He kicked out at the invisible monster, wanting desperately to escape but he couldn't. He had no one and he knew it. He was alone. Abandoned. No one was coming for him.

"I can tell you believe me," the Colonel whispered in his ear, "You just don't want to admit it." The Doctor struggled against the Colonel's grip, shaking his head rapidly. He wasn't going to believe it, he couldn't. Donna will come back for him. He was the only one who could take her home. Except Jack could easily take her home as well. Jack had a vortex manipulator...that could take him to any time period and Donna only had to ask. The Doctor felt all the air rush from his lungs. The thought felt like a punch to the guts. She wouldn't...would she?

The Doctor held back tears, feeling alone and abandoned. "But you have the Underground now," the Colonel stated. The Doctor felt his stomach turn sour and bile rise up his throat. No matter what happened, he knew he didn't want to be part of the Underground. He would escape even with the knowledge of Donna's abandonment. "We gave you shelter, put food in your stomach, and clothes on your back and you've been nothing but difficult with us. Your behavior has been spoiled and because of that I've been forced to punish you." The Doctor glared at the Colonel. "You need to learn...understand that we are all that you have left and the sooner you except that. The sooner your life will get easier."

The Doctor nodded his head, anger raging through his chest. It was the type of deadly anger that he felt towards the Daleks. The anger that drove him to destroy planets and end dictatorships. The anger that gave him the name the Oncoming Storm or the Destroyer of Worlds, but he didn't know where he was directing it. That anger had been trapped for a very long time and now it was finally bubbling over the top. He didn't want any of this. He dreaded the thought of a life within the Underground. No freedom. Just pain and suffering and he didn't want that. He felt the collar cringe underneath the strength of his anger and slightly spark. The Colonel watched as his eyes turned a deep black and the pupils a bright gold, a sick fascinated smile twisting Graham's features. But as soon as it started, it had ended. The collar blasted him with a powerful electric current, shutting down all his abilities once more and leaving him dazed against the chair. The Doctor heard a slow, sarcastic clap and he glanced over at the Colonel.

"Another thing about that collar," the Colonel stated, "If it even gets the feeling that your abilities are awakening it gives you a sharp shock to end your concentration and shut them back down. I have to say, I'm quite impressed with how much thought the scientists put into that metal contraption." The Doctor glared at the Colonel, with hate-filled eyes. He was tired of it. He was emotionally and physically drained and just wanted it all to end.

The Colonel grinned wolfishly at the automatic reaction. It was the type of reaction he wanted. The hate and anger was part of creating the perfect assassin. And the Time Lord would be an excellent assassin, probably better then the ones they had now. All the Colonel needed to do was take control of the Time Lord's rage and use it accordingly. The raw power he felt in the room brought shivers to his spine and that's what he wanted with every weapon they created. He scratched at his skin and more chunks fell off. The Colonel gritted his teeth in disgust.

The Doctor noticed the chunks and his attention immediately left his dark thoughts. His full focus was on the skin that laid on the table and the Colonel itching rapidly. He lifted a curious eyebrow and the familiarity of solving a mystery fought back the darkness that wanted to consume his soul. His brain quickly mapped out everything he knew about the Colonel. From the first time he met him until now. He licked his lips fascinated about the skin peeling off the Colonel's arm and he glanced around the room trying to find more evidence to conclude his hypothesis. He knew he was right. He always was and if so, what the Colonel was doing to himself was extremely dangerous and could have fatal affects.

The Doctor's eyes landed on the waste basket where four syringes sat on top a pile of papers. Every thought popped into place. Why the Colonel felt different to him but still had the human elements, the aggression, though he was an aggressive man beforehand, the snarling and predatory feel that emanated and sent shivers down the spines of others, and every other strange occurrence. The sunglasses, the gloves, the shedding skin it all added up and the Doctor bubbled with excitement of finally solving a mystery that had been driving him nuts. It was so stupidly obvious that he smacked himself in the head and turned a knowing gaze at the Colonel.

"I know what you did," the Doctor stated, "And what you are doing to yourself is dangerous." The Colonel faced the Doctor, a scowl on his face.

"Was I speaking to you animal," he growled, "Because I don't believe I was. So, shut-up." The Doctor clamped his mouth shut. He shouldn't say anything, it would only get him into trouble, so he didn't. If what he believe was true, then any provocation caused would only set him off. The Colonel had killed Jake and the other soldier that much was obvious. He noticed the covered up bloodstains on the carpet and the bleach that was meant to clean the stains off. Even without his senses, he could smell the fear that was in the room previously and the dangerous energy that the Colonel gave off. The Doctor glanced over at the Colonel and noticed a hint of a brownish-green that the Colonel was trying to hide under his long shirt.

The Colonel for the past couple months or so had been dosing himself with a concoction of different alien DNA. The Doctor didn't know why, but he felt like the plan was pretty obvious. The Colonel, from what the Doctor could figure, was trying to become what he considered superior. Better senses, strength, speed, and whatever else that would be useful to his goals for humanity. But from the peeling skin, sunglasses, and gloves the Doctor could guess what was happening. The Colonel was changing physically, gaining some of the characteristics that the alien DNA he used had and it was changing him.

"Why," the Doctor asked aloud, "Why are you doing this to yourself?" The Colonel spun quickly around, facing the Doctor. A hateful sneer lifting his top lip and his fist clenched.

"I thought I told you to shut-up," He growled, "Apparently you're to stupid to understand that." The Doctor sat up straighter, a determined look in his eyes. He wanted answers and he was going to get them, even if he was punished for it. But why should the Colonel care? He was just an alien and no one ever listened to him anyways.

"Please answer my question," the Doctor stated, "I know you know what I'm asking." The Colonel glared, teeth gritting in anger. He bent down low, getting into the Doctor's face. The Doctor didn't flinch. He didn't care anymore. He had nothing to lose.

"Did you just order me, freak," the Colonel hissed. The Doctor stared right back into those covered eyes.

"No, I asked you a question," the Doctor replied, before giving a cheeky smirk. "Don't worry you can tell me. No one would listen anyways. Like you said I'm just an alien. Nothing important." A fist slammed into his face and the Doctor heard his jaw crack under the pressure. He doubled over in his seat as another blow hit him in the guts. The blows kept coming, each one more vicious then the next. Finally the last blow was given and the Doctor fell over exhausted. His face was covered in dark black bruises, as well as his torso, and other parts of his body that was hit painfully. The Colonel twisted his fingers into the Doctor's hair, yanking him up.

"You want to know why," he growled, jerking the Doctor's head a bit. "I'll tell you why." The Colonel's hot breath touched the Doctor's ears as he leaned in closer, his lips next to the Doctor's ear. The Doctor gurgled in pain as blood dribbled between his lips. The Colonel's beating had opened up old wounds and blood drenched his shirt.

"The human race needs a bit of a boost," the Colonel snarled, "And I'm willing to find that boost. We need to show aliens who's boss and what better way then to strengthen our abilities. The only people we can trust is each other because aliens..." The Colonel tugged on the Doctor's hair, initiating a hiss. "Are..." The Colonel stood up, pulling the Doctor up to his feet by his hair and unhooking his hands from the desk. "Backstabbing..."He dragged the Doctor over to the middle of the office. The chair he was chained to, dragging behind him. "Freaks that need to learn who's in charge." He released the Doctor's hair, pulling out a tiny tuff of brown fluff. The Doctor collapsed to the ground and the Colonel unhooked him from the chair. The Doctor glanced up, touching the now bald spot on his head.

"So, I'm correct then," the Doctor stated, "You created a dangerous serum to enhance human abilities to match that or above that of other extra-terrestrials."

"It's a horrible universe out there and humans need to get to the top," the Colonel confirmed, "Even if it means we perform some despicable acts." The Colonel sneered, before a sinister smile crossed his features. "Don't worry, we'll be good masters to those inferior races. We just need to cut down about half or more then half of them." The Doctor glared, knowing exactly how the Colonel planned on cutting down.

"It's a big universe out there," the Doctor replied, "People won't like being ruled by you. There will be revolts." The Colonel squatted down next to the Doctor.

"Why do you think I'm creating biological weapons," the Colonel stated, "Or the serum. Or allowing the scientists to learn everything they can about the aliens we capture."

"You're no better then the Dalek you killed," the Doctor icily stated. The Colonel stiffened at the insult, glaring down at the Time Lord with contempt.

"I don't like your attitude," He stated, "I think you're in need of a bit of discipline. Take off your shirt and roll onto your stomach. If you fight, I'll just call in the guards to hold you down." The Colonel proceeded to remove his belt and the Doctor glanced over in shock and fear. He wouldn't...would he.

"What are you..." The Doctor was kicked in the side.

"I gave an order and you better obey me," the Colonel stated as he folded up his belt, smacking it down in his hand. The Doctor rolled onto his stomach, silently pleading to whatever great universal watcher was out there. The Doctor heard footsteps trudging in as the office grew more crowded with people. He could smell humans and aliens alike in the room. Apparently they brought in the other prisoners they captured to give a demonstration of what happened when you disobeyed. The Doctor felt the hard leather smack his back. He winced but couldn't help the relief sigh that passed his lips. But there was no guarantee that they wouldn't one day do what he feared. The Doctor counted each lashing he was given, his face pinking with humiliation from being on public display, during his punishment. Yes, he was going to get out with or without Donna Noble's help. He had his TARDIS to save as well as the universe.

* * *

The UNIT campground was teaming with life as Donna walked through the set-up. She had sent the five aliens she, Jack, and Ama had rescued over to Kurt, who quickly fixed up their injuries. At the moment Donna wandered aimlessly through the campground, her mind jumping from one train to another but all lead to the same worry. The Doctor. She couldn't help but worry about her poor Spaceman. He had already been through a lot in the past two and a half months and to be there for another week or so must be excruciating. She couldn't help but wonder if he questioned her loyalty because she was sure a place like that would cause that to happen. She sighed heavily and strode over to the strategy tent, where many of the UNIT soldiers were in, planning the next attack.

The team, that she sent out some time ago, had finally returned but they brought back disturbing news that unnerved the Torchwood and UNIT teams. Apparently, when they arrived on the scene where the assassins were killed. No one was there. Not one dead body. It was like they vanished into thin air. The only reminiscence of death was the blood that soaked the forest floor. There was a lot of arguing about what happened and everyone concluded that the aliens couldn't wake from the dead, but that hopeful conclusion was brought to utter destruction when Roc and Tak walked in on the discussion. They had told the group that the assassins never really died, unless the Underground wanted them too. They were always brought back to life before being sent out on other missions. It was a sick cycle and Roc didn't know how many times the assassins were brought back from the dead, but if it was anything like Jack's immortality then it was unlimited until the Underground found a way to permanently terminate the weapon. Donna hated thinking like that, but that's what the assassins were. Weapons. And she couldn't help but fear the fate the Doctor would have if they didn't rescue him in time.

Donna stomped into the tent, her hands in her pocket. She was enveloped in a giant hug and lifted off her feet. She glanced up to find Jack's winning smile and she couldn't help but grin back.

"Hey you," she asked, "What's up?" Jack put her down, his grin widening.

"Everything's great,"he exclaimed, "Guess what Donna, we're getting the Doctor tomorrow! We can finally shut that place down, rescue the Doctor and the others, and say good riddance to all the bastards that started that place."

Donna raised an eyebrow. "Really? What's the plan then?" She stood, glancing around in anticipation.

"Thanks to Jake," Jack began, "We have all the information we need. We can weaken the security, send in our alpha team which will be Torchwood and a few UNIT officers, the beta team will enter the back way and we'll surround the employees of the Underground before sending some of our men out to find the other aliens." Jack danced around a bit, antsy for action. "Piece of cake. We'll get the Doctor out in no time at all." Donna frowned. She liked the plan but there was one more element they were missing.

"What if they are moving that day," she asked, "The trucks and aircraft, whatever they use to transport the aliens. What then? We'll miss them by seconds." Jack glanced up as if deep in thought before turning away from Donna and running back over towards the group of men, who sat around the blueprints. Donna crossed her arms as she watched Jack spout his concerns and the expressive hand gestures of the men around him. After a while Jack came running back over with a smile on his face.

"All set. We're going to have two more teams. One team will be in a helicopter and we'll also have the UNIT airforce on the ready. Another team will be waiting by the Underground parking garage in trucks, blocking the exits. Either way they can't escape." Donna nodded her head and Jack grinned charmingly. "Anymore concerns, beautiful?" Donna rolled her eyes and gave a playful smile.

"Not at all. In fact, it sounds like you've got this all planned out," Donna stated, "Except one request." Jack quirked an eyebrow.

"Yeah," he asked. He waited for the answer already having an idea of what the demand would be about.

"I'm coming with you," She stated, "I'm going to be by your side the whole time and be one of the first to find the Doctor. I am not going to sit around here like a lazy nervous lump, waiting for the men to return. Got it?"

Jack nodded his head, his eyes sparkling with amusement. "Well can't argue with that," he stated, "Welcome to the team Ms. Noble." Jack playfully shook Donna's hand, before their faces contorted into a more serious expression.

"We'll be leaving early tomorrow," Jack explained, "I've already told the others the plan and everyone's game." Donna glanced down at the ground, wringing her fingers nervously. Jack placed a comforting hand on her shoulder. "Is everything alright?" Donna nodded.

"Yeah...yeah everything's fine," she said, "I'm just dreading the thought of seeing the Doctor tomorrow. I know his conditions going to be bloody awful but Jack what if he isn't even the same person anymore? What if he's already become one of those assassins?" Jack shook his head and pulled Donna into a comforting hug, he placed a soft kiss on the top of her head.

"Donna don't worry," he said, "The Doctor's made of tough stuff. I don't think a few humans will change his beliefs. Even if they did, we'll be there for him and pull him out of the dark corners of his mind. Donna I promise you, no matter where you go, I will always be there for you and the Doctor." Donna nodded her head, leaning into Jack's chest and melting into his comforting embrace.

"Promise," she asked. Jack smiled, before stepping back and looking Donna in the eyes.

"Yeah. Cross my hearts and hope to regenerate," Jack stated, doing the hand motions as he quoted their favorite Time Lord. Donna chuckled and slapped him playfully on the arm, before sighing deeply and rubbing at her eyes wearily.

"The Doctor always says that," Donna responded. She felt the tears prickle in her eyes. "I miss him a lot." Jack nodded his head solemnly.

"Yeah," he said, "Me too."

* * *

** I hope you enjoyed this nice long chapter. :) Please tell me what you think. I have nothing else to say. The next chapter will probably be the first part rescue chapter, following by the second part. I thank you all for following this story. There's at least five chapters left, so the story is coming to an end. Please review and tell me what you think. :)**


	42. Chapter 41

**Thank you for all the incredible reviews. They are so encouraging to me and it makes me happy to see them in my email! Thank you again! So, here's the next chapter and I hope you enjoy. Please review and tell me what you think! Warning there are some stronger swear words then before. I don't know why I'm warning you guys, but I guess it is polite to warn people who don't like reading crude words.**

Chapter 41

Donna was dressed in black ops garment. Her ginger hair was pulled back into a ponytail as it swung back and forth to the beat of her march. Her blue eyes searched the surroundings as men and women alike loaded up the large trucks. The soft morning breeze brushed her face and the sky was a light black, with the sun slightly peaking over the hilltop. It was the morning they were going to save the Doctor and everything was set in motion from the looks of it. Their surveillance team had been watching the building the Underground laid beneath and had not witnessed any changes in the Underground's beat. But they had only seen the surface action while underneath everything could be moving quite differently. The sonic boom shook the ground and Donna glanced up, noticing several UNIT military aircrafts fly overhead, the smoke trailing behind it as the planes twirled. Donna smiled knowingly. Yes, they were going to get the Doctor out. She just knew it.

"Donna!" Ama yelled, running forward. The girl skidded to a stop in front of the woman in question. In her hand a beaded necklace with different exotic patterns was twisted around her fingers. "Here," she stated, handing the necklace over to Donna. "I made this for you. It's a Shian luck necklace. It's meant to keep you protected and give you good fortune with your quest." A sheepish smile crossed Ama's face and her eyes turned down embarrassed about the gift she was giving. She scratched the back of her neck as her blue cheeks turned a light purple. "I t-thought you might need it you know. To keep you safe and everything." She looked away from Donna's blue eyes, biting her lip in embarrassment. "I just want to make sure the Doctor is rescued and in my culture the necklace ensures good luck and safety so I thought it appropriate..." Donna cut the girl off by pulling her into a hug and kissing the crown of her head. She took the colorful beaded necklace from the girl and smiled warmly as she put it around her neck and tucked it into her black uniform.

"I love it sweetheart," Donna replied softly, "It's a beautiful, thoughtful gift and I'll hold it close forever." Ama smiled, nodding shyly before hugging Donna once more.

"Thank you,"she said. She pursed her lips, nibbling on her cheek as she planned on what to say next. She sighed, concluding on the two words that would sum everything up. "For everything." Donna nodded her head in understanding.

"It's alright sweetheart. It's what me and the Doctor do and I am so happy I met you even though the circumstances weren't the greatest."

Ama smiled. "I would've still been there if it wasn't for you or the Doctor. You two saved my life and excepted who I was and I wish I could repay you. I would love to come and help..." Donna shook her head, brushing the white strands out of Ama's face.

"No Ama, I don't want you to come with us and you have no reason to repay me," Donna said, "I want you to stay here and keep everyone safe. Be on the look out for danger. I promise you when we return we will take you home. You will see your family again Ama." Ama nodded her head, hugging Donna once more.

"Ok, I will," Ama said, her voice choking on the held back emotions.

"Well if it isn't two of my favorite women," Jack exclaimed. He wrapped his arms around Ama's and Donna's waist and kissed them both on the cheeks. "What are you two plotting?" he wiggled his eyebrows and gave a playful flirty look. Donna grinned back, before smacking him on the chest.

"None of your business Captain flirts-a-lot. It was private matters," Donna retorted and Ama shyly smiled at her two friends.

"Is it private matters I would enjoy taking part in," He asked, with a flash of his white teeth and wink of an eye. "Because Ms. Noble I'm willing to help with any issues you may be suffering from. I'm really good at that." Donna laughed, giving the Captain a one arm hug. Ama covered her mouth, trying to hide the giggle.

"You know I'm wondering why you said two of my favorite women. What's that suppose to mean," Donna stated. Donna knew very well what the captain meant. But he was purposely trying to distract her and Ama from the dark thoughts that surfaced ever so often in their minds and she was grateful for Jack's effort. So, she willingly went along for the ride, playing along with his flirtatious game.

"Because you are," Jack replied before getting a sly smile and what Donna liked to call his flirty eyes. "I like a lot of women but you two are top of my list." Donna rolled her eyes and slapped him on the arm.

"Oi you, just for that you can forget the kiss I was planning to give you," Donna playfully stated, "You're not getting anything out of me sunshine." She had no intention of kissing Jack...well, that was a lie. She had thought about it several times, especially when he went into 'protecting his friends' mode. She always liked a man who was willing to lay down his life for his friends and Jack was definitely one of those types.

"You were planning on kissing me," Jack exclaimed, before rubbing the back of his neck. "Oh darn I ruined that hopeful fantasy." Donna chuckled, crossing her arms, and giving a playful stern look. Ama stomped over and stared right up at Jack.

"Well,I didn't make or break any promises," Ama murmured. She grabbed Jack by his coat lapel and pulled him down, meeting his lips. Jack at first looked a little startled from the sudden force of the normally quiet girl, before he relaxed, enjoying the kiss. He felt Ama's mind touch his and he shivered as her mind stroke certain pleasure points that made him weak at the knees. Yep, he definitely liked telepaths. Top of his favorite list for sure.

_Why thank you Captain Harkness,_ Ama stated in his mind, _I think I like boe-kind as well. _He felt Ama's mind pull away from his as reality fell back into place. A satisfied grin stretched across Jack's face and his knees wobbled from the sudden pleasant experience. Yes, definitely liked telepaths. He glanced over at Ama's glowing features, as she softly crossed her arms.

"That was called a Shian good luck kiss," She stated flirtatiously, "Maybe later I'll show you how the Shian says congratulations." Jack nodded his head rapidly, his eyes still dilated and a dreamy look on his face. Donna laughed at the look. It was quite obvious Ama did a number on the normally not flustered Captain.

"I would like that," the Captain replied. He felt slightly dizzy and off-balance which was quite rare for the Captain, but he forgot how much effects psychics had on him. He straightened up, striding over to Donna.

"We should get going," He stated, "I want to get the Doctor out of there and fast. The trucks are waiting and the teams are set. Just stay close to my side and I promise you, you will be safe." Donna nodded her head.

"Alright lets get moving then," Donna stated. She stepped over to Ama and gave her a hug. "Be safe and keep everyone else safe. We'll be back in no time." Ama squeezed her eyes shut and hugged Donna back. She pulled away, stepping back.

"I will,"she replied, "Just go. Get the Doctor back. We'll be fine here." Donna turned away, heading towards the truck. Jack winked at Ama, a flirty smile curving his lips.

"I expect that congratulations when I get back," He replied playfully, "Take care Ama." Ama nodded, wrapping her arms around her stomach. A shy smile flitted across her lips before she turned away from her friends.

Donna and Jack jumped into the truck with the Torchwood team and several UNIT officers. Donna couldn't help but notice the absentminded look on Becky's face as she twirled a pocket watch between her fingers.

* * *

The Doctor was yanked off his bunk, rough fingers twisting around his arms. He fell to the floor in an exhausted, bloody heap and refused to move another step. The session with Colonel Graham had taken a lot out of him. He had fought back, but because of what Colonel Graham had done to himself, it made him incredibly strong and able to outnumber the Time Lord's own strength at the moment. Which if you looked at recent events was quite pathetic and embarrassing for the Time Lord.

"Get up alien," a guard ordered. A hard kick was driven into his side and the Doctor steadily stood to his feet. The room spun from the sudden head rush he suffered from and he took a deep gulp, trying to get his equilibrium back intact. He shook his head, clearing out the stars, before immediately noticing the crate that sat next to his cell.

"What?" he asked, stepping back. No, it couldn't be. They couldn't already be moving. It was just yesterday when he heard the Major and guard discuss it. He didn't even have time to think up a clever plan of escape. He backed slowly away, but the guards grabbed his arms tightly and began dragging him forward. No, he wasn't going to leave. His eyes searched the room, trying to find the best way to escape without being stopped.

"That's right freak, we're leaving this joint," one of the guards growled, while trying to force the Doctor forward. "Maybe if you behave, I'll ask the Colonel to give you a nice cell at the next place." The Doctor shook his head rapidly. No, he didn't want a nice cell, he wanted to be far away from these people. His hearts quickly picked up speed as panic overtook him. He didn't even notice the painful twinge in his back as his ripped muscles stretched uncomfortably because of his squirming. His eyes frantically darted around the cell-block. He felt like a cornered animal unable to escape and his teeth gritted in fury and fear. With a sudden lurch, he threw himself to the ground dragging the guards down with him. He kicked out, catching one in the guts, before throwing a punch at another. He didn't care if this was against his morals, he couldn't move...he just couldn't. He heard shouts and his cell became more crowded with soldiers. He howled in frustration as they pounced on top of him, trying to restrain him and drag him forward. A hand moved over towards his mouth and his teeth snapped at it. The salty, metallic taste of B positive blood filled his mouth as a howled scream and colorful stream of cuss words left a soldiers mouth.

"Fuck! Son-of-a-bitch bit me," the soldier screamed, "I think it ripped off some flesh!" The Doctor didn't care, he was frantically trying to escape the grabbing hands and he let out another angry howl. He wasn't going into the crate, no matter what. He swung his fist and it connected with something soft and solid. He really couldn't see who he was fighting off, all he knew was that he was in danger and needed to run. He yanked away from the arms, jumping to his feet, and bolting out his cell door before someone tackled him from behind. The Doctor heavily fell to the ground. Several other soldiers jumped on top of him, trying to restrain him. He screamed in a mix of anger and agony and clawed at the floor, trying to escape. He gritted his teeth and released a bloodcurdling growl from the back of his throat. He was not leaving. He felt two men tug at his arms and he lashed out hitting one in the face and kicking the other. Even if it meant he had to die, he was not leaving. He continued his slow crawl out of his cell, knowing the collar would go off. He didn't care anymore, he was not going to be a weapon. His face was slammed into the floor as he felt a group of men drag him back in. He hissed, eyes slitting dangerously. He struggled using everything he had. He bit down on someone's arm, kicked, scratched, punched, kneed, head-butted, whatever he could do to escape, but the soldiers kept coming back and more held him down. He didn't realize, even in his weaken state, how much power he had when he really didn't want to go somewhere.

"What is the meaning of this," a voice shouted. The fight froze as everyone turned their gaze to Dr. Morley, who was standing there arms crossed. The Doctor's moan was muffled by the gag between his teeth. During the fight, someone had managed to gag him to stop him from biting the others.

"Dr. Morley, Ma'am we were given orders to pack subject 13 up for the trip," one of the guards stated.

"It just didn't want to go into the crate," Another stated, "It was being difficult." Dr. Morley glanced over at the Doctor, who was breathing heavily. His eyes crazed from the adrenaline rush and soft choked coughs caused his adam's apple to bob.

"It attacked us first, Ma'am," a third explained, "It went all psycho and I think it tried to commit suicide." The Doctor closed his eyes, breathing heavily through his nose. His eyes snapped open and darted around the room, still searching for a way to escape and he slowly began to struggle against the tightening grips of the soldiers.

Dr. Morley nodded her head, before stepping forward. She glanced into the Doctor's sweaty, red face and undid the gag. The Doctor immediately launched at her, causing a few of the guards to stumble as they tried to hold him back. Dr. Morley took a couple of steps back. The Doctor's eyes squinted darkly and his lips curved in a snarl as he struggled against the guards grips. A sharp slap made contact with his face and his struggles immediately froze as he stared at Dr. Morley in shock. He couldn't believe she actually slapped him. She never hit him before. Dr. Morley stared him down with a cross look.

"That's quite enough from you mister," she reprimanded him like a misbehaving child. The Doctor's mouth gaped at the tone she was using and he nodded his head slowly. He felt the guards slightly relax their grip and he considered making a break for it but knew they'd probably stop him before he even made it to the door. Dr. Morley pulled out a syringe and a bottle, her look stern. "Are you going to behave yourself?" she asked, "Because if you're not. I'll be forced to drug you and I don't want to do that because I know you're capable of being civilized." The Doctor nodded his head, eying the drugs suspiciously. Ever since his first session with Dr. Black, he was terrified of all unknown substances which was bad considering what he did for a living.

"P-please I d-don't want to go i-into the c-crate," he pleaded with Dr. Morley, "I-I'll b-behave myself. I promise." Morley raised an eyebrow and shook her head.

"Sorry subject 13 but you have to," she replied, "It's procedure." The Doctor backed away slightly, eyes wide though the guards held him still. "Hey, hey,shhh...calm down," Dr. Morley cooed softly, brushing a hand through his hair. He flinched from the touch, struggling against the guards grips once more. "Subject 13 relax," Dr. Morley said in a stricter voice, "I will not drug you if you get into the crate willingly." She cupped the Doctor's chin and ran her thumb comfortingly along his jawline. "I'll be next to you the whole time. Nothing to fear. We're just relocating and you'll have a new cell quite soon. Isn't it exciting! A new place to live in."

The Doctor shook his head, pulling away from her grip. He didn't want this. The guards had relaxed their grasps, feeling the Doctor slowly calm down. He was still tense but he had no other way to escape. "Now you can either get into the crate willingly or we can drug and force you into it," Dr. Morley stated, "It's your choice. Either way you're getting into that crate." The Doctor sighed, walking slowly over to the crate. The guards followed him, making sure he wouldn't try to run. One of the guards shut down the movement grid on the collar, allowing the Doctor out of his cell. The Doctor stared at the tiny crate, humiliation at being packed away like some dog caused a choking bulge to form in the back of his throat.

"Get in the crate," Dr. Morley ordered. All the guards stood around, guns and cattle prods in hand. The Doctor sighed, falling to his knees. He proceeded to crawl into the box that was the size of a large dog kennel and curled up into a ball as the metal door was slammed shut on him. He looked through the metal wiring of the door as the guards lifted the crate he was in and placed it on the trolley cart. He bumped his head as they wheeled him out the door. He noticed, for the first time, how empty the Underground was.

* * *

Jack drove quickly down the road, taking sharp turns as he tried to race the clock. Donna banged her head against the wall of the truck, before accidentally smacking Becky. Becky and the other people in the truck held on for dear life. Some gritted their teeth in fear and shock, while others mouths gaped at the sudden turns, letting out a fearful shout once in a while. The wheels squealed against the ground as Jack took another sharp turn. Everyone bumped their heads that time.

"Sorry," Jack shouted. Becky rolled her eyes.

"Do you mind slowing down a bit," she exclaimed, "I'd rather not die from an accident you know. Personal preferences and everything. Plus, who would save the Doctor if we died in a fatal crash." Jack glared at her through the rear view mirror, before making another sharp turn and squealing to a stop in front of the paper company building. The group listened to the other trucks surrounding the building and the clipping sound of a helicopter flying overhead. The paper company was somewhat outside of the city and sat on a large patch of land with a large parking lot. Jack scanned the area, waiting. He heard his group jump out of the back of the truck while Becky and Donna sat patiently waiting for Jack's orders.

The sound of a large truck was heard and Jack's eyes narrowed. Some of the team members were already breaking down the paper company doors and flooding into the building.

"Donna was that the parking lot you escaped through," Jack asked. Military crafts flew overhead, searching the air for any illegal planes. Donna glanced over and nodded her head.

"Yeah," Donna stated, "Why?" Jack revved the gas, a grim smile on his lips.

"Hold on tight," Jack stated,he slammed his foot on the gas and the truck went squealing forward. Donna couldn't help but scream at the sudden burst of speed and Becky held on tight to her chair. A truck at that moment pulled out of the parking garage and Jack hit it full force. There was a squealing of wheels and the sound of metal scraping against metal as the truck Jack hit rolled over from the sudden force. Smoke billowed out from the truck and Donna could hear the screams of fear coming from it. UNIT officers immediately surrounded the fallen truck and pulled out the drivers. They opened the back, finding a bunch of aliens in crates, squealing and chattering in fear. A UNIT officer gave Jack the thumbs up and Jack jumped out of his truck, helping Donna and Becky out. The rest of the alpha team followed.

"We've got to move fast," the officer said, "they've alerted the others. They were transporting the first group of aliens. It looks like everyone is fine back there but Dr. Parker and a team of UNIT medics are going to start checking them over."

"Was the Doctor in the truck," Donna asked, "She glanced worriedly at the truck as aliens were helped out of the back. The officer shook his head.

"Then that means he's still down there," Donna stated. She glanced over at Jack and he nodded in understanding.

"Alright everyone," Jack shouted, "You know the plan. Move." Donna led Jack and the others through the parking lot and over to the hidden staircase. One of the members quickly blasted it open and the group ran through the opening. The alarms were blaring as the group ran into the organization as heavy doors slammed shut behind them. They quickly made it through the emergency shutdown. They entered the white hallway of the Underground and quickly spread out. Becky ran down a flight of stairs, heading towards the computer room with a group of men by her side. She was going to stop the alarms and open up the emergency doors for the other teams. The soldiers held heavy shields as they protected her from the heavy rain of bullets and tranquilizers, quickly pulling her out of the way of traps. Jack, Donna, and several others ran down the opposite hallway. It was weird the place seemed empty which shouldn't be possible unless they already moved and that was the last truck. In that case they had already missed the Doctor.

Jack raced down the hallway, tailcoat flapping behind, he skidded to a stop and Donna almost ran into his back. He tapped his vortex manipulator and a grin crossed his face.

"Found you," he exclaimed, "This way." he took a right and Donna followed the sprinting captain, the other soldiers close behind. The blaring alarms had turned off thanks to Becky and they were no longer shot at by guns and other weapons that were secured into the walls. Jack threw himself against a wall slamming Donna next to him. He pulled his gun out as he heard the loud clomps of men marching by. Donna could tell that the Underground soldiers knew they were under attack, the raised weapons and cold looks was evidence enough. Donna's eyes widened in recognition as Major Johnson marched pass.

"Jack," Donna whispered, "That's the Major I was talking about." Jack nodded his head and lifted his gun. Bang! The shot hit the Major in the shoulder and everyone immediately opened fire. The fire battle was short lived as the UNIT team proved to be more prepared. Jack grabbed the Major by the collar of his shirt, yanking him up. Their noses touched and the captain growled.

"Where is the Doctor," Jack snarled. The Major kept his mouth clamped shut as he moved a hand to the bloody wound in his shoulder. The other UNIT soldiers ran down other hallways, looking for other possible ambushes or trapped aliens.

"Gone," the Major stated coldly, "Not here anymore. We killed it." Donna gasped, covering her mouth. She wouldn't believe it. No. He was lying. She marched over and landed a sharp slap across his cheeks just as Jack threw him against the wall and held him tightly.

"You better be lying," Jack hissed, "Because if you're not, you will learn the true meaning of pain when I'm through with you." Donna glared coldly at the Major.

"He's lying," Donna responded, "The Underground wanted the Doctor for a reason. They wouldn't just kill him." Jack nodded his head, before banging the Major hard against the wall.

"You better tell me," Jack ordered, "Or else." The Major stared coldly at the Captain, gritting his teeth stubbornly. Jack pressed a finger into the Major's wound, initiating a hiss.

"Jack stop it," Donna ordered, "Don't be like him." Jack glanced over at the paled face Major and nodded his head. He loosened his grip, but still held him threateningly tight. At that moment Jack's vortex manipulator went off, alerting him to the Doctor's presence. He released the Major, who crumpled to the floor. He pointed in the direction they needed to go, before he looked down at Major Johnson, who's shirt was sticky with blood. Donna ran in the direction he pointed and Jack turned from the Major.

The Major reached for his fallen gun, his hand shaking in pain. He lifted the gun and pointed it at Jack. Jack turned around hearing the click of the safety switch turning off. He pulled out his gun, _bang,_ and shot the Major through the head. Major Johnson slumped against the wall. Eyes glassy with death. Jack turned coldly away and pocketed his gun. He stuffed his hands into his pocket, a grim look on his face.

"That's what happens when you hurt my friends," he muttered, before racing off after Donna.

* * *

The Doctor smacked his head against the ceiling of the crate for the umpteenth time. The group of soldiers that escorted him were wheeling him quickly down the hall and turning quick corners as they tried to make it to the aircraft they were going to escape in. Many of the scientists had already packed up their stuff, but apparently Dr. Black and Carter were trying to organize themselves still. Dr. Morley strode along next to the cage, keeping a careful look out for intruders. She had expected the attack and wasn't surprised when the alarms screamed before shutting off quickly. One of the guards radios blared.

"_The trucks have been cut-off, I repeat the trucks have been cut off. UNIT has blocked off the exits and Military crafts are patrolling the air. The base is surrounded." _Dr. Morley nodded her head at the announcement, quickly turning down another corner.

"Come on we can still get Subject 13 out safely," she stated, "We have other ways out and the Colonel only wants subject 13, if we can't get any of the others out." At that moment the sound of gunfire echoed through the room. Twenty UNIT men jumped out, pointing their guns at the Underground employees. Shouts of 'freeze and surrender' surrounded the employees and the Doctor couldn't help but smile at the sight of UNIT's logo. He gave a relief laugh as the UNIT soldiers began handcuffing the guards. One of the UNIT officers bent down and looked into the crate. The officer's eyes widened and he quickly saluted in excitement.

"Sir, Doctor, it is an honor to meet you sir," the officer exclaimed as the others carted the arrested employees off. Morley glanced over and couldn't help the smile that curved her lips. It was interesting seeing a human get all flustered about meeting an alien. Subject 13 must have been an important creature if this was the reaction he recieved. "I'm sorry our meeting had to be under these circumstances." The officer unlocked the cage, helping the Doctor to his feet. The Doctor nodded his head and rubbed the back of his neck awkwardly.

"Yes,quite right," he murmured, "And please don't call me sir."

"SPACEMAN!" The Doctor turned towards the familiar nickname. He could hear gunshots in the background from the UNIT soldiers' invasion, but no longer were the alarms blaring. Somebody must of shut them off.

"DOC!" Donna plowed into his chest in a loving embrace, his shirt growing wet from her tears. Jack came running after her with matching exuberance as he embraced the Time Lord as well. The Doctor was wobbly at the knees from months of abuse and he could barely stand but he wanted to hug his companions. The weights of the last months finally lifting. His eyes prickled with tears and a sob escaped his lips. That's when the last two and a half months came crashing down. He fell to his knees as sobs wracked his body. He covered his face in humiliation at having the UNIT officers witness his weak state. He felt soft human arms wrap around his neck and a soft kiss placed next to his ear as Donna comforted him. She whispered soothing words, rubbing circles on his back. He glanced up at her a watery smile cracking his face.

"I knew you'd come back," he whispered. Donna kissed him on the cheek.

"Always," she replied, pulling him into a hug once more. She couldn't help but frown at the hard cold metal that pressed against her chest. She had not noticed the collar around the Doctor's neck until now and it made her blood boil with anger. But she didn't say anything about it. She didn't want to upset the Doctor. The Doctor pulled away, grinning a relief smile but everyone in the room noticed the haunted look in his teary eyes. Months of torture did that to a person, even a Time Lord.

"Hey Doc," Jack stated, "Long time no see." The Doctor glanced up at the immortal, a huge smile on his face. He wobbly got back to his feet and threw his arms around Jack's neck. Jack wrapped his arms around the Time Lord, holding him up in a comforting hug.

"Thank you," the Doctor said, sniffing. Jack patted him on the back. The Doctor glanced up into the Captain's blue eyes, a cheeky smile tugging at his lips. "About time you got here. What took you so long?" Jack laughed.

"Sorry, we got stuck behind some obstacles," Jack replied, "But we made it through." The Doctor nodded as Donna laid her head softly on his back.

"What about the other Underground employees," the Doctor asked, "they might escape." Jack shook his head.

"No worries. There's a whole army out there arresting people right now," Jack replied, "Just relax. Someone's looking for the Colonel right now." The Doctor stiffened and immediately stood stalk still.

"No Jack," the Doctor said, "Don't let anyone go after him. They'll be killed."

"What do you mean Spaceman," Donna asked.

"Remember when you were telling me how you thought something was wrong with the Colonel. Well there is," the Doctor responded, "Colonel Graham has been injecting himself with a serum created with different types of alien DNA. He wants to strengthen human abilities, make them stronger then the average extra-terrestrial. He's highly aggressive and only I can stop him." Jack watched the Doctor transform from a broken man to instant hero in mere seconds. His whole stance had changed, but Jack knew this would be short lived.

"What is Graham planning," Jack asked. The Doctor shrugged.

"Meh...the normal take over the universe and enslave the inferior race plan," The Doctor replied, eyes darkening. "But he might succeed."

"Why's that," Donna asked, "We stopped him didn't we."

"Yes, but the Underground has been building their own man-made diseases," the Doctor stated, "I figured it out after my third escape attempt. I found a file about man-made diseases and other dangerous viruses. On my first escape attempt, I met some of the plague carriers. What the Underground is planning to do is send those plague carriers back to their planets. The disease they created is a more advance version of frencidous with other little diseases added in. And because it is a whole new disease entering the ecosystem, the disease would spread rapidly without a known cure. Many will die. Graham wants to cut more then half of the population in the universe down."

"Frencidous is a deadly disease to begin with," Jack commented, "But how is Graham planning on changing the human race." The Doctor shrugged.

"I think he might also send the virus throughout earth. There was something about controlling diseases. If Graham could, he would decide on a specific target to attack, in this case sentient non-human people. He would release the disease and the disease would infect everyone with non-human blood. But to answer your question Jack, the serum is a clear liquid form, how would you change the human race?"

"Through the water supply," Jack answered. The Doctor nodded grimly.

"But the serum, I don't believe its complete. It has terrible side affects and I believe the Colonel is changing into some type of monster."

"Thought he already was," Donna muttered.

"And if the serum is given to every human on the planet they'll probably have the same deadly side affects," Jack concluded, "Great all in days work I suppose."

"I'll go after Graham," the Doctor said, "Stop him from escaping. You guys rescue the carrier aliens and destroy the disease the Underground created. I want everyone else making sure no one escapes. Find the prisoners and help them. Whatever needs to be done." The Doctor took a step forward before falling to his knees in pain, all the wounds that covered his body made him weaker, thanks to the collar canceling out his healing abilities. He could hear one of the UNIT officers relaying all the information on the comm link but everything was blurring. Donna helped him back to his feet and he clutched at her shoulder, muscles straining in agony.

"Doctor what do you need me to do," Jack asked. The Doctor glanced over at Jack, his mouth gaping like a fish. Donna hovered around her two boys, worried and wanting to help.

"Take the c-collar o-off," the Doctor stuttered out, "a-and l-let m-me h-heal."

"How," Jack asked, frantically looking for a button, "I don't see anyway of taking the collar off." The Doctor hissed again from the pain in his back. He had forgotten he was still injured from all the excitement of today.

"A remote. The Colonel has a remote. So does the scientists and...and Major Johnson," the Doctor explained, his teeth chattered in agony as his body screamed in distress from all the movement. Jack jumped to his feet, leaning the Doctor against Donna, before racing off down the hall. He passed UNIT soldiers, marching by and arresting people. He skidded around a corner, finding Major Johnson's body where he left it. He stuck his hand in, rummaging through the dead man's pockets, his hand curled around something metal as he pulled out the remote. Jack jumped back to his feet and raced back to the room, skidding to a stop. Donna, the Doctor, and several other UNIT guards watched the panting captain as he waved the remote about in a 'found it' gesture.

"Which button do I press," he asked. The Doctor shrugged his shoulders, gritting his teeth in agony.

"I don't know," the Doctor sarcastically stated, "I never thought of asking." Jack nodded his head.

"Ok, then I guess I'll just have to test out some of the buttons," Jack decided. The Doctor glanced at him wide eyed.

"Jack don't...just don't...AHHHH!" He was cut off as electricity raced through his body. Jack dropped the remote in shock, before fumbling to pick it up. The Doctor twitched on the floor as electricity burst through his nerves, before the pain finally subsided.

"Doc...Doc I'm so sorry," Jack exclaimed, "I didn't know..." The Doctor shook his head, cutting Jack off.

"Let's not press anymore buttons alright," the Doctor stated through chattering teeth. Jack nodded his head, handing the remote guiltily over to Donna. Donna glanced over the remote and shrugged.

"Beats me, I don't know how to shut it off," Donna stated, "We need some technological genius to look at it and right now I don't think the Doctor is up to fixing anything at the moment." The Doctor gave a strained laugh as his hand shook from the residing electricity. At that moment the doors banged open and Becky came sprinting in.

"Hey, everyone. I've shut down the whole organization. Right now the security is down and UNIT is coming in and destroying research," Becky stated. She glanced over at the sprawled Doctor on the ground. "Oh, hello you must be the Doctor. I'm sorry we didn't arrive sooner."

"No problem," The Doctor stated through gritted teeth, "Just been hanging around, having a real party. By any chance do you understand technology b-because at the moment I am incapable of rewiring the remote and shutting off the damn collar."

"Ummm...yeah, I guess," Becky stated. She pulled out a screwdriver, flipping it in her hand. "Show me what needs to be done."

"Donna h-hand her the remote," the Doctor ordered, spittle covered his lips, "please." Donna gave Becky the remote and immediately she opened up the back and started rearranging the wires. The Doctor felt the collar snap off from around his neck and fall to the side. A relief sigh passed his lips as all his Time Lord abilities returned to him at full-burst. The Doctor felt his skin slowly heal and patch back together again. He could feel the timelines of everyone in the room and his old strength and speed returning. He slowly sat back up, a somewhat satisfied grin on his face.

"Well, I feel physically better," the Doctor exclaimed. He jumped to his feet, slightly cringing from his slightly tender muscles. "Oooo...that was not wise. Not wise at all. I should take it a bit slower."

"Doc, if you can't," Jack began, before clamping his mouth shut as the Doctor gave him a threatening glare.

"I'm fine Jack. I am going after Graham and stopping him," the Doctor stated determined, "You find the diseased aliens, stop whatever evil plot the Underground is planning, etc..." The Doctor sighed. "Afterwords, I'm going to find the TARDIS, get everyone home, and forget about this place." Jack raised his hands in surrender at the Doctor's icy tone. He already could tell that the Doctor had changed quite a bit from what he used to be. The Doctor limped over to the door, his wounds already healing before everyone's eyes.

"What is everyone standing around here for," the Doctor barked, "We have an evil organization to shut down and people to save. Now move!" Everyone jumped into action and the Doctor turned a corner, heading in the direction where he sensed the Colonel was.

* * *

**Thank you for all the wonderful reviews. They are really encouraging and I am happy that people want me to continue. :) At the end of this story, I will tell you the next few stories I'm planning to write. These stories will probably be updated slower then the Underground, probably only a couple chapters a week, thanks to my for now on busy schedule. I hope you review and tell me what you think. :)**


	43. Chapter 42

**Thanks for all the wonderful reviews! :) That's all I have to say...Hope you enjoy this next chapter. :) Please review! I love reviews!**

Chapter 42

Colonel Graham quickly marched down the halls, black suitcase in hand. He headed towards a secret exit, that only he and a few of the scientists knew about. The attack from UNIT, to him, was not a surprise at all. They've been a pain in his backside for too long. Plus with the traitorous guard contacting them, the Colonel had foreseen the attack, that's why he wanted to leave quickly. He just didn't expect UNIT to be so organized and prepared this time as well as unpredictable. They had brought the whole damn army to tear apart his organization and he wasn't going to allow it. Colonel Graham quickly turned a corner before marching straight and turning a left. Maybe he'd kill off UNIT first...and possibly Torchwood. Unlike the rest of the world, they couldn't see the benefits of his plan. They wanted to be forever controlled by aliens. But that was all going to change. The human race once again would be at the top and aliens from all planets would bow down before the superior race.

Inside his bag held the serum vial he and a couple scientists had created. He had volunteered to be the first test subject for the serum that would change the world and he loved it. The serum made him feel powerful, like he could do anything he wanted with no consequences to hold him back. He could go back in time and save his family. Of course he couldn't physically do that, but if he could break into subject 13's ship and learn how to fly it, he could go anywhere he wanted and save his family from their tragic death. Colonel Graham gritted his teeth in determination at the plan. No, UNIT will not stop him. He will succeed. Colonel Graham turned another corner, his knuckles white from the grip he had on the bag. Of course his plan made sure he was the most powerful out of the whole human race, so he could easily overthrow uprisings and other sort of rebellions.

He wasn't a stupid man, he had learned from history how most dictators failed and he wasn't going to make the same mistake. He had already taken part in uniting the human race against aliens with the acceptation of a few ignorant idiots. He would strengthen the human race physically and soon mentally and together they would overthrow the universe. It made perfect sense. Colonel Graham turned another corner, his footsteps clipping silently on the floor. Too bad UNIT had to come here and mess everything up. They probably are destroying the virus they created right now. No matter, he'd just dispatch a few assassins to deal with them. If worse comes to worse the Underground could start from scratch.

But he wasn't going to start from scratch with the human race. As the Underground rebuilds the virus, the human race could learn about their new found abilities and he could be their teacher and by the time they finished they could take over. Simple as that. They had alien spacecrafts, alien weapons, their biological weapons, and their new found superhuman abilities, nothing would be able to stop them. All he had to do was send the serum through the water network and Europe would be the first to change, following Asia and then the United States and once those Major continents were changed. They could transform Australia and then the islands. Of course the serum wasn't designed for aliens and actually had a toxic side affect on them. The Colonel made sure the scientists laced it with a poison that was only deadly to aliens. In that case, if the alien drank the water, it would instantly die.

The Colonel turned right. He had avoided every single UNIT soldier in this place. He was first going to retrieve the blue box and then he would escape. He'd find another way to capture subject 13 later. It wasn't going anywhere without its ship. The Colonel skidded to a halt when he saw a group of soldiers standing around the door that he needed to enter. The door led to the room that held the blue box. The guards had already got it set up for transport and all he had to do was get it to the exit and head to their new base. Yes, he would need to start from scratch, knowing that most of his employees were either dead or arrested. He'd probably have to find new aliens as well and train them himself. New assassins were always beneficial to his cause. Maybe he'd do the breeding program that Dr. Carter proposed. Weapons from scratch. Colonel Graham lowered his briefcase, setting it gently on the floor. He removed his gloves, exposing sharp, deadly claws meant for slicing through soft flesh. The claws always added a more menacing approach to things. The claws clicked together as they extended to their full length and the Colonel removed his sunglasses to reveal yellow slitted eyes that were once blue along time ago.

The eyes were what scared people the most. It sent them falling to their knees, pleading for mercy and the Colonel loved it. He loved the fear and the begging and the screaming in pain. It aroused him. He silently stepped over to the unfortunate men and with a snarly hiss and deadly click of his teeth, he plowed his claws into the first mans guts, ripping out his insides. The hysteric screams surrounded the Colonel and the fire of guns echoed through the room. He avoided everyone of those bullets, leaving a trail of carnage behind him. His bones cracked painfully as his body began to change. Whenever he overexcited himself his bones snapped and began to stretch and poke out of his skin. But recently his skin had been rotting and falling away in chunks, leaving a greenish, gelatine type covering over his bones. He just blamed it on the metamorphosis of his new and improved body.

The Colonel slid his claws out of the last soldiers body. Blood smeared the walls and the ground and the soldiers body laid twisted with silent screams on their faces. Chunks of their flesh was missing and blood matted their hair. The Colonel turned away from the carnage and quickly picked up his briefcase. He gained access and stepped through the door, where the blue box sat,chained to a large trolley cart.

"Hello my beautiful prize," the Colonel growled, "We're going to travel the universe together. All you have to do is open your doors." He heard with his more acute hearing the angry hum that came from the ship. Before when he was just a normal human, he couldn't hear or smell the life signs coming from the ship, but as everything advanced, he could sense everything. That's why he ordered the scientists and guards to torture the ship. He wanted to break it, make it bend to his will and make it except that it belonged to him. But like pilot like ship, it proved to be stubborn and hold its grounds. He strode over, a sick smile on his face. He laid his hand on the blue exterior, before yelping in surprise as it shocked him. He snarled, shaking his hand. "I'll take care of you later," he threatened. The response to his threat was a defiant hum.

He grabbed the trolley's handles and began wheeling it towards the secret exit. The room was huge with poles and staircases and ramps leading to exits. He marched over to the door, opening it and leading the blue box out. The hall they walked down was wide and on either side rails lined the wall, water rushed underneath the path. He wheeled the ship over the bridge before stopping at a second door, he quickly opened it and inside the new room was an aircraft that flew faster then any earth military craft ever created. The aircraft again was designed by Underground scientists, who had used alien technology to make the superior plane. He was going to escape and all his plans could soon be put back in motion.

"Impressive craft you have there," A voice stated behind him, "I bet it flies quite beautifully. Great for a quick escape." Colonel Graham turned to face the voice, knowing exactly who it was.

"Subject 13," he growled. Subject 13 skipped down the couple steps, hands behind its back, and a grin that didn't quite reach its eyes on its face.

"Yep. Well, I prefer the Doctor actually," Subject 13 responded, "Sort of the name I chose you know."

"How did you find me," the Colonel snarled. He watched as subject 13 circled him with a predatory look in its eyes. The Colonel flexed his claws, he wasn't going down without a fight.

"The carnage outside the door was a dead giveaway," it responded, "Plus the door opening up to an impressive escape route and you wheeling my TARDIS away was another." The Colonel growled tensing for a fight. He wasn't a stupid man, he knew subject 13 was highly dangerous when not controlled.

"I'm going to guess you're here to stop me," the Colonel stated. Subject 13 nodded his head.

"Yes," he replied, "Because what you're about to do will kill the whole human race." Colonel Graham snarled, just like an alien to tell him he's wrong. Subject 13 just wanted to gain control that's all. It has no idea what it's talking about.

"No," the Colonel sneered, "I'm making the human race stronger. So, they can defeat animals like you." Subject 13 shook its head sadly, stepping forward cautiously as if approaching a wild animal.

"You're dying," it stated, "The serum is too strong for your body and it's killing you slowly. Yes, it strengthens your abilities, but your skin is rotting and falling away and your bones are cracking and contorting. Whenever you strain yourself or gain to much adrenaline you're body deteriorates quicker. Do you really want to do that to the human race? Make them suffer and die. You'll be the cause of their extinction."

The Colonel paused for a second, thinking over what subject 13 said, before the familiar, irrational anger returned.

"No, you're lying," The Colonel shouted, "It's just a metamorphosis. The beginning of a new and powerful being." Subject 13 shook its head.

"Really its not," it replied calmly, "It will be the destruction of the human race. Millions...billions will die including other lifeforms because of what you did. Just stop this and give me the briefcase. I can help you."

"No!" The Colonel launched forward, his claws outstretched as he tackled subject 13 to the ground.

* * *

Jack, Donna, and a group of UNIT soldiers ran down the windy corridors. It made Donna just sick from all the loops and turns. The Doctor had given Jack all the information he had on the alien carriers and the other diseases and now they were racing over to destroy evidence and whatever launch ships they have and hopefully help the ill aliens they tested the disease on.

They had skidded around another corner when they heard the Doctor call their names.

"DONNA! JACK! I STOPPED THE COLONEL! LETS GO HOME NOW!" Jack glanced over at Donna and Donna back at him. The voice sounded like the Doctor, but didn't have the same caring tone the Doctor normally had in his voice. Jack lifted his gun, pointing it in every direction. He glanced back at the UNIT soldiers.

"Everyone be ready," he ordered, "That voice is not the Doctor's and I know exactly what it is." Donna glanced around searching the halls. The lights had begin to flicker and the hallways grew darker. All she could hear was the heavy, fearful breathing of the soldiers as they prepared for the unknown. Sweat beaded Jack's brow and Donna glanced around for something to fight with. A soldier tapped her on the shoulder, handing her a baton and she nodded her thanks. Even if she couldn't fight the monsters off, it was nice to have some protection. The lights overhead finally flickered off and everything quieted.

"WHERE ARE YOU GUYS! I'M REALLY SCARED AND WANT TO GO HOME! PLEASE TAKE ME HOME!" Donna scooted closer to Jack. Not that she was afraid or anything, but unlike Jack she wasn't immortal. They couldn't even hear the patter of footsteps on the hard ground or see the assassin. They didn't even know how many were coming or if they were armed and dangerous. But judging from last time, Donna and Jack knew they were dangerous and ready to kill.

"WHERE ARE YOU!" it sing-songed before getting a mock sad voice. It pulled at Donna's heart just hearing the words coming from the Doctor's voice. She knew it was a guilt tactic, but she couldn't help but feel depressed. "DONNA YOU PROMISED TO COME BACK! WHY DIDN'T YOU COME BACK AND HELP! THEY HURT ME DONNA! I BLED ON THE FLOOR, BEGGING FOR MERCY. BUT YOU NEVER CAME TO MY RESCUE! WHY?" Donna swallowed heavily, clutching the baton close to her chest.

"Shut-up demon," one of the soldiers shouted. His hand trembled in fear. They heard a dark chuckle, echo down the room.

"AND JACK! YOU SAID YOU LOVED ME, CARED FOR ME! WHERE WERE YOU! WHERE WERE YOU! I WAS AFRAID, SO AFRAID!" Jack's hand trembled with anger as the monster spouted out all of his concerns. Jack clutched his gun, his knuckles whitening from the tensity.

"BUT NOW I HAVE TO KILL YOU ALL! YOU ALL BETRAYED ME!" The voice grew closer, but they still couldn't hear the footsteps. "I was alone," a voice whispered behind them. Every soldier turned around, seeing a cruel, hateful smile cross the creatures face, before in a blink of an eye the assassin was gone. Donna's heart jumped to her throat, she felt like prey in the middle of the night, unable to escape the predator.

"There it is," someone shouted and suddenly guns were firing rapidly and Jack pulled Donna out of the way and pushed her against the wall.

"There's another one," another soldier shouted. Bullets flew in every direction and the gunfire lit up the assassins face. They were just as horrendous as before and Donna recognized one of them from her first encounter. The assassins dodged each bullet with ease. Swinging their arms and killing a couple of the soldiers.

"Donna stay there," Jack ordered, "I want you safe. I'm going to try and kill a few of them." Donna nodded her head, gladly staying out of this one. She would love to help, but she had no fighting skills whatsoever. She might ask the Doctor at some point for some martial arts training, just so she could defend herself. She ducked just as a bullet smacked the wall above her. Jack stood in front of her, shooting at the aliens tumbling through the air. How could you kill something that couldn't die? Unless, they could die and the Underground had some type of machine or remote control that keeps the body moving.

"Jack," Donna shouted. Jack glanced at her before turning his gaze back towards the battle.

"What Donna, I'm sort of busy at the moment," Jack stated a little more harshly then he needed to. He was under a lot of pressure.

"I just had a brilliant thought about how the aliens are staying alive," Donna stated. Jack remained silent, but Donna knew he was listening. "What if they really are dead and it's just their bodies you are fighting. The bodies have no souls, its just a walking, talking dead guy. Sort of like a vampire mixed with a zombie."

"A zombie," Jack answered sceptically.

"Yes, a zombie," Donna snapped back, "It makes sense. Remember the difference between the two aliens. Three of them looked completely dead, like something from a horror movie while the one in the forest looked whole. It was beautiful and enchanting, but didn't give you nightmares because of disgusting appearances. I was thinking what if they all started off like that beautiful assassin in the forest, but when they died the Underground didn't want to get rid of them because they were running short on assassins, so they created something to keep the body animated and alive, but the soul and what made the assassin a person was long gone. They still have all their skills, but don't have the emotions to make a sentient being."

"So, you're saying the dead looking assassins are actually dead and just animated flesh," Jack concluded.

"Yep," Donna replied, "Is there any alien tech that can keep a dead body alive and kicking." Jack's eyes widened as he fired off a couple more shots.

"Yes, actually there is," he stated, "and they quite possibly could be using it. It's from the planet Retcon 9. The planet is constantly at war and they don't have a lot of soldiers. So, what they do is stick these ear monitor type things into the ears of their dead soldiers. The ear monitor has a wire that shoots out and climbs up the ear canal, connecting to the brain, and with a sharp jolt of energy they reanimate the body. It can fool people into believing they are actually still alive. They normally have the one personality trait they died with, so if they died insane, they would be insane now. They can have conversations and give fake feelings and have all the normal motor skills but they're still dead. Their flesh rots away, making them look like zombies."

"How would they gain the 'bring me back to life' ear things though," Donna asked, "If the planet is at war."

"A transport ship could of crashed," Jack replied, "because Retcon 9 is on one side of earth while the planet their fighting is on the other side. So they are constantly flying back and forth over our galaxy. When it crashed it must have had boxes of those."

"Then we shoot them through the brains, right," Donna said, "That would kill them."

"Worth a shot," Jack stated, "maybe aim for where the temporal lobe is. That's most likely where the attachment is connected." Donna nodded her head. Jack shouted out the orders and the new plan and all the soldiers aimed for the head. Some of the assassins were already falling down dead.

* * *

The Doctor spun out of the way as the Colonel swung his clawed hand. He ducked and dipped and danced out of the way of every swing. He could smell the exhaustion, washing off the Colonel and knew he was tiring, but was too stubborn to stop.

"Colonel let me help you," the Doctor begged, "We can end this. No one else needs to die." He flipped out of the way as the Colonel threw a heavy arm in the Doctor's direction.

"Yes someone does need to die," The Colonel snarled, charging forward and slamming his fist into the Doctor's gut. The Doctor sailed through the air, hitting the aircraft with a hard thunk. All the air rushed out of his lungs and his respiratory bypass system turned on. Colonel Graham stalked heavily forward, sweat beading his brow and hatred and insanity coloring his yellow inhuman eyes. "You." He slammed his fist into the Doctor once more, his claws digging into the Doctor's flesh. The Doctor screwed his eyes shut, gritting his teeth against the pain. His eyes snapped open and he slowly began crawling up the side of the aircraft's wall using the Colonel's strength to hold him up. He began pushing the Colonel back with his feet, removing the claws from his gut and tumbled to the floor, before rolling out of the way of the Colonel's heavy feet.

The Doctor jumped back up, slightly stumbling from the loss of blood. He breathed heavily and continued to dodge the Colonel's punches and attacks.

"Let me help you," he said again, "I can get the serum out of your bloodstream. You don't have to die." The Colonel didn't answer instead throwing another punch, which the Doctor dodged easily. The Doctor clutched his stomach in agony, but he kept fighting. Why did he always deal with creatures with claws? The Doctor danced out of the Colonel's reach, turning and spinning from another possibly fatal blow.

The Colonel collapsed to the ground, screaming and the cracks of bones and cartilage echoed through the room. The Colonel had been leaving a trail of rotting flesh in his wake and in its place was green goop. The Doctor sadly watched the transformation, knowing the green goop was the serum eating away the Colonel. The serum was spreading rapidly through his body, thanks to the Colonel's adrenaline rush. The Colonel crashed against the craft, shaking. An insane smile on his face.

"I can feel it. I'm growing stronger," the Colonel shouted. His bones cracked some more and one shot out of his skin, causing the skin to fall apart and blood to drip from the wound.

"No," the Doctor said sadly, "You're dying. The serum is eating away at your flesh. Please let me help you." The Colonel shook his head, getting back to his feet and stumblingly charged at the Doctor.

"You're just in denial," the Colonel growled, "You don't like the thought of me being stronger then you." He swiped slowly at the Doctor and the Doctor twisted his body out of the way from the attack. The Colonel screamed again, clutching at his head. Green slime mixed with blood dripped from his mouth. The Doctor stepped forward, bending down next to the Colonel.

"Because of your hatred, you're dying from your own creation," the Doctor stated, "If you had chosen to move on with your life, instead of taking your anger out on aliens. You might still be healthy with a new life, one not filled with hate."

"I can still kill you," the Colonel growled. He lurched forward, only falling to the ground once more as more skin rotted and fell away. More bones stuck out of his back and blood seeped from his wounds. The Colonel heavily breathed in pain, all the strength and speed he once had gone.

"Then I can not save you," the Doctor replied, pressing down on his injured stomach. "I'm sorry. So sorry about what happened to you and your family but you made the wrong choice and now you're suffering the consequences."

The Colonel let out a blood chilling scream and the Doctor backed away. He couldn't save him, the Colonel had made his choice. The Colonel writhed on the ground as his flesh fell away and his eyes bulged and popped out. The serum ate away at his flesh quickly and the Colonel's body suddenly bulged into green ooze. _Pop!_ The colonel's whole body burst into green liquid and washed over the floor. All that was left was an abnormal pile of bones.

The Doctor glanced sadly at the bones, knowing it used to be a man. A corrupt man but a man altogether. "I'm sorry. I'm so sorry," the Doctor stated, "Why does everybody die?" The Doctor fell to his knees, his abdomen bleeding rapidly. He let out a pain-filled howl as tears fell down his cheeks. Yes, the man had tortured him horribly, but he was still a human being who deserved to live. No one deserved to die, especially like that.

_Theta._ The Doctor turned his head to his ship, he could still feel the pain she suffered from and immediately all the guilt came rushing forward. _Come here sweetheart. _The Doctor steadily limped forward, picking up the black briefcase with the serum in it. He glanced at his TARDIS who was chained to the trolley cart.

"I'm so sorry. I'm sorry I couldn't stop them from..." The Doctor choked on his words and the old girl hummed softly. _It's alright. We'll heal together and Donna will help. You are not alone, Theta. Allow your friends to help you._ The Doctor nodded his head and slowly began undoing the chains. The TARDIS doors snapped open and the Doctor stumbled in. A sigh of relief passed his lips as he fell into his captain seat. He glanced around the console with all the buttons and levers. He was finally safe and home.

* * *

The Assassins were dead. The soldiers had shot each one in the head. It took a while but they had gotten a few lucky shots. Jack had gone around looking for the Retcon 9 technology in the assassins ears and grimly concluded he was correct about the theory. The Assassins now laid dead and Donna couldn't help but cry when she looked into their finally peaceful faces.

They can finally rest in peace without the worry of being brought back to life. She couldn't help but wonder who they used to be before they were changed into the monsters they were now. They could have had families out there. Children. No one would've known what happened to them and that made Donna sad. Jack wrapped his arm around her waist and led her away from the bodies. She sniffed slightly as they walked towards the pathogen room.

Jack opened the door and the smell of sickness immediately blasted their nose. Jack saw the freezer shelves packed with containers holding samples of diseases and on the other side, neatly packed in cages, awaiting transport were the diseased aliens. The aliens laid curled in their cells, none moving because of how deadly sick they were. Donna covered her mouth, tears sliding down her cheek. These people had suffered long enough and it was time to let them go.

More soldiers came marching in, they banged open the door at the far end, opening it up. Inside was several alien spacecrafts, all with destination coordinates typed in and a place for the diseased aliens to be place in. the ships were created in a way that allowed pathogens to escape and spread quickly. It would've infected whole planets. Also in the room was a counter with different chemicals boiling inside a flask. They had found notebooks confirming the Colonel's whole plan. Immediately a toxic waste clean-up crew had arrived and began taking pictures and packing away the dangerous viruses for study purposes. Afterwords all the evidence would be destroyed.

Donna Noble slowly walked over to the sick aliens, they backed away from her, pressing up against the wall.

"Hey, don't be afraid. I'm here to help," Donna stated. The alien curled up in a ball and a whimper exited her mouth. "Please don't cry. We'll find a cure."

"There is no cure," the alien responded, "We're going to die to frencidous plus several other diseases."

"But..." Donna started, her voice started to choke with emotions. "I want to help you."

"Then let us die," the alien said, "Let us go." Donna nodded her head.

"What do I have to do," Donna asked. The alien glanced up, sighing sadly.

"When you get what you need," the alien explained, "Set this place on fire. Blow it up. Kill the disease."

Donna sighed heavily, wiping the tears from her eyes. "Alright I will." She glanced over at Jack, who stood behind her a grim expression on his face. He pulled Donna over, hugging her as she cried into his shirt.

"Thank you for your kindness," the alien said sadly. She curled up in her cell, blood dripping from her eyes, nose, ears, and mouth. Donna nodded her head as fresh tears fell down her face.

"Come on Donna," Jack said, "Let's get out of here." He carefully lead her out of the Underground. Soldiers ran back and forth collecting evidence and arresting the criminals.

* * *

**Thank you for all the wonderful reviews. There are three to four more chapters left of this story. I hope you review some more and tell me what you think. :)**


	44. Chapter 43

**Thanks for all the wonderful reviews! They make me really happy when I see a new one in my inbox. They encourage me to update. :) Thanks again! Well, here's my next chapter. Hope you will all enjoy! **

Chapter 43

Donna glanced around worriedly at the Underground site. She had not spotted the Doctor yet and dread filled her heart. He was already weak to begin with and the thought of him going after the Colonel in his weak state terrified her. The wind rustled her ponytail and her arms folded over her chest, trying to stay warm. She watched as UNIT soldiers ran in and out of the building, collecting needed evidence, and loading up the criminals. They were setting up explosions in the Underground to blow it up, so no one would ever go back to it and they could burn the disease from existence. A tear curved down Donna's cheek as she thought about the poor aliens that suffered from the abuse and disease. Now they were just going to die without anyone trying to help. She knew they didn't want to live anymore, but this was no way to die. To be blown up with the building. She understood the soldiers reluctance of touching them, do to the lack of information they had on the virus, but couldn't they just kill them beforehand instead of blowing them up.

Donna wiped the tears away. She hated that place so much. They had suffered at the hands of evil people and now it was over. It was kind of hard to believe but it was all over and she could now figure out a way to heal her Spaceman. She knew it would be a long journey, but she was going to be by his side no matter what. Donna sniffed and let out a choked sob. All she wanted to do was go home and she planned on doing just that. She was going to have the Doctor take her back to her time period and convince him to stay. She knew her Mum would be a little reluctant about letting the broken man into her home but she would change and become instant nagging mother figure towards him. She was sure of it. Also, having her Grandfather around was good as well. Her Gramps had a more patient and gentle demeanor then her mother and he would provide the comforting support the Doctor needed. Overall, she needed to go home and heal. It had been a long two and a half months and she felt like she aged a few years. She needed to get out of 2015 and soon. Yes, she loved Jack and the Torchwood crew but it was time for her and the Doctor to heal as well and the best way for that was with her family.

Her plan was settled, after the Doctor and her dropped off the aliens to their home planets, she and him would go back to 2009 and spend a few months on earth recuperating. No adventures, no danger, no pain or fear or trying to save a planet from an evil dictator, just coming to terms with what had happened to them and being there for each other. She needed it and he most definitely needed it even if he wouldn't admit it. Donna wrapped her arms tighter around her chest, the wind had picked up with an icy chill in the air. Her nose had turned a bright red from the cold and crying. All she wanted to do was go home.

"Hey beautiful," Jack's voice whispered behind her, "What's wrong?" She turned around to face Jack's blue eyes. She wiped at her nose and turned into Jack's chest for comfort. He immediately wrapped his arms around her.

"He's not out yet, Jack," Donna murmured, panic evident in her voice, "He's not out. What if something happened to him. When we found him, spaceman wasn't doing to well. He was weak and hurt and what if he didn't make it out alive..." Jack cut her off, hugging her tightly.

"Donna please don't worry," Jack replied, "The Doctor is strong. Look what he's been through and he's made it out alive. Yes, we'll be dealing with a broken Doctor for a while but he will get better. I just know it." Donna shook her head, fresh tears streaming down her face.

"Jack, I need to go home," she whispered, "I can't handle this year anymore. I need to go home." Jack nodded his head in understanding.

"Alright, what about the Doctor," Jack asked, though he already knew the answer. The memory of Donna striding into the Torchwood base when he first met her with the Doctor trailing behind hit him hard. He remembered how the Doctor glanced around nervously at the high-tech room and jumped when loud noises startled him, holding on tightly to Donna's hand. His previous team had been out, dealing with a rift issue so he was alone with the Doctor and Donna. He knew that this memory was connected to this event. He was going to help the Doctor and Donna even if it was in his past and their future. Time travel was a confusing thing even for an ex-time agent.

"I'm going to convince him to stay with me," Donna stated determinedly, "He needs the help and I need the help, what better way then among friends and family." Jack smiled, holding Donna closer. She knew what was best and he trusted her judgment.

"Visit me alright," Jack stated, "Even if I don't know who you are. Let me know what happened to the Doctor so I can help. I want to be there for you two."

"Alright," Donna stated, a soft smile curving her lips. "That will be a strange encounter. Me meeting your past self. I'll know a bit about you and you'll know nothing about me. Time travel is so weird." Jack chuckled.

"Yeah, just a bit." Donna buried her face into his coat, sighing deeply. She yawned widely as her exhaustion finally caught up with her.

Her eyes began drifting shut when the familiar sound of whirring, groaning engines caused her eyes to snap open. Jack smiled as a blue box materialized in front of them, before stopping with a sudden thunk. The two companions stood outside the TARDIS doors, waiting for the Doctor to appear. Donna tapped her foot in anticipation and kept taking nervous glances between the TARDIS and the Underground base. The doors opened and the Doctor stumbled out, falling to the ground. His mouth gaped in pain as he slowly dragged himself up. Donna and Jack ran over helping him to his feet.

"Oh, God!" Donna cried as she noticed the blood gushing from the wound in his stomach. His eyes were dilated and his skin an icy pale. Jack took off his coat immediately and pressed it against the Doctor's injury, trying to stop the bleeding. The Doctor cried out as his wound stung and his teeth chattered in pain.

"Donna go get Kurt or someone," Jack ordered, "We need to sew this up and bandage it." Donna nodded her head in shock before she ran over to the medical tent that they had set up an hour ago.

* * *

The UNIT doctors and Kurt were briskly fixing up the freed prisoners injuries. There was a lot of fear among them and some cried out in panic as a doctor approached them with a needle. They had brought in volunteered help to try and comfort the distress aliens as they fixed up their wounds and gave them a brief check-up.

Kurt was currently busy, helping an alien who was suffering from a broken leg. His leg was broken in three different places and Kurt didn't want to know the cause. The alien was one of the aliens that escaped the first time when the Doctor had let everyone loose, but was caught a few days later by the Underground soldiers. There were other aliens who had been captured quite recently, probably only a few days before today. They weren't in terrible shape, but they still faced possible trauma disorders just because they were in the Underground for that amount of time. Overall, the little medical clinic they had created was quite busy, thanks to injured aliens and soldiers alike.

"KURT!" Kurt turned his head to Donna's shout, he quickly handed over the supplies to his assistant and quickly walked over to Donna.

"What's wrong," he asked. He turned around just as he heard someone, possibly one of the aliens, scream out in pain and fear. There was a lot of quick whispers and hushing voices as they tried to calm the startled alien down.

"It's the Doctor," she stated out of breath, "He just came out of the Underground and he has this huge gaping wound in his stomach. He collapsed on the floor and Jack at the moment is holding him up and trying to stop the bleeding. He needs immediate medical attention and fast." Kurt nodded his head, grabbing his medical bag. He alerted one of the UNIT doctor's to his patient over in the corner, before he headed out the tent.

"Did you try moving him," Kurt asked as he spotted Jack in the distance and a blue box standing tall behind him. Jack was crouched over a man sprawled on the floor, his coat pressed against the man's abdomen.

"No, we were afraid to," Donna responded, "He was bleeding a lot. We did get him to his feet, but it looks like Jack laid him back down." Kurt nodded as he slid next to the pale figure. Jack nodded his head at Kurt, before stepping back. He carefully touched around the wound before pulling out his medical bag.

* * *

The Doctor opened his brown orbs, breathing heavily through his mouth. He dazedly watched a man, he did not recognize, open a medical bag. The Doctor's eyes widened as the man pulled out a needle and he felt his hearts pound quicker. His breathing become more shallow as the man lowered the needle towards his stomachs. He had to escape...he just had to. He didn't know what was in the vial and it could hurt him. The Doctor let out a high-pitch struggled screech as he kicked out violently, hitting the man in the guts. He screamed as he tried to roll away and climb to his feet but the amount of blood he lost made him weaker and he fell back to the ground. His writhed on the floor as he rapidly pleaded in Gallifreyan. He struggled as he felt two pairs of hands hold him down and he cried out again, fear driving him to fight back. They were going to hurt him again. He knew it. He didn't do anything wrong, so why were they punishing him. Maybe if he begged they'd let him go.

"Please," he pleaded, "Please let me go. I'll be good. I promise. I didn't mean to...p-please let me go." He felt the hands soften their grip but still held firmly, pinning him to the ground. He felt fingers gently brush back his hair and a soft kiss placed on his forehead.

"Doctor don't panic, it's just us," a familiar voice stated, "It's just me and Jack. Remember we rescued you. You collapsed in our arms a few minutes ago. You're safe." The Doctor blindly searched for the voice. His eyes had blurred thanks to the pain in his abdomen and he couldn't tell if it was reality or if he was hearing voices.

"Oh, bloody hell," a new voice muttered and the Doctor jumped as he realize somebody was prodding his abdomen. The scientists. He begin struggling once more against the tight grip, begging for them to stop.

"Doc, Doc calm down," another voice said. The voice sounded like Jack even felt like Jack. It must have been Jack. Was Jack letting the scientists hurt him? He wouldn't...would he? "Doc, don't worry. It's just Kurt, he's going to stitch up the wound you have. Make you better." the scientists had stitched up the wounds he collected, but they always hurt him again. Maybe this was what this Kurt was doing, fixing him so they can tear him open again. The Doctor again struggled against the hands that held him down. Suddenly a man with mocha colored skin and corkscrew curls arrived in his line of sight. The man had a gentle face and kind eyes and the Doctor immediately relaxed. The man wasn't going to hurt him.

"Hey Doctor," the man, Kurt, said, "I've heard a lot of great things about you. Jack never shuts up about how you save the universe and how great you are." The Doctor nodded his head, a suspicious look still in his distrusting eyes. But if Kurt knew Jack maybe he wasn't so bad.

"How d-do y-you k-know Jack," the Doctor asked. He glanced around for the first time realizing he was outside with Donna and Jack on either side of him. They smiled comfortingly, but their sad, pity-filled eyes didn't escape his observation. He hated pity.

"I work with him," Kurt replied. He wasn't looking at the Doctor anymore, more focused on cleaning out the wound and stitching him up. The wound just needed a bit of help to heal properly. The Doctor nodded his head, distracted by Kurt's talking.

"Oh," he said, "You work for Torchwood then." Kurt nodded his head, smiling.

"Yep," he responded, "I hear you travel through time and space with Donna. Maybe you can tell me what that's like."

"Lot's of adventures," the Doctor stated. He didn't know why, but he felt like he could trust this man. Maybe it was the kind eyes.

"And running," Donna added, smiling at the Doctor. His eyebrows were scrunched up in concentration. He wasn't paying attention to the needle that was sewing him up. Which was a small mercy since he was so terrified in the beginning. He had a right to be scared though with everything he's been through. It would take a lot of little steps to get him back to the way he was, but she could do it.

"All done," Kurt stated with a smile. The Doctor startlingly glanced down at his abdomen that was neatly patched up with a white bandage over it. He didn't even know that Kurt was sewing him back together. He slowly sat up, noticing he didn't feel any pain in his abdomen or anywhere else.

"Why?" he asked, looking curiously around at the three humans. Kurt smiled, packing his equipment away.

"I gave you a pain-killer," Kurt responded. He noticed the Doctor's eyes widening and softly shook his head. "No worries it wasn't aspirin. Jack warned me about your allergy." The Doctor took a relieved sigh, leaning back down. The Doctor heard the soft clips of military boots on the ground and he immediately cringed, expecting a swift kick to the guts.

"Captain Harkness, sir," the soldier stated with a salute, "Brigadier Jameson wanted me to relay information about our foundings and the proceeding plan that we have decided upon. Sir." Jack nodded his head, gently rubbing comforting circles on the cringing Doctor. He glanced down concerned when the Doctor didn't make a witty, sarcastic retort about the saluting or the soldier's manners. Donna held the Doctor's hands, feeling his body convulse in shutters at the close proximity of the soldier. Jack stood up, placing his hands behind his back, waiting for the soldier to continue. The soldier cleared his throat.

"We have found all the alien's records and DNA samples in the lab," the soldier relayed. Jack was about to interrupt when the soldier continued. "But what we couldn't find was any records on the Doctor or the DNA samples they would've collected. Everything about him was gone, including anything about Donna." Donna stood up,causing the Doctor to jerk in surprise from the sudden quick movement.

"What do you mean my DNA samples are gone," she shouted, "They didn't collect any samples." The soldier shook his head, backing slightly away from the angry ginger woman.

"Yes, they did Donna," the Doctor stated, "Remember Carter." Donna's eyes widened and she covered her mouth.

"That brings me to another issue," the soldier replied, "It seems we did not find and arrest everyone."

"What do you mean," Donna growled, "I saw you arrest them. You were loading up a bunch of those terrorist in the back of your truck and carting them off to UNIT's prison until further notice."

"Yes, but it looks like several people escaped," the soldier stated, "The following escaped members were Dr. Richard Berrings, Dr. Jordan Sprite, Dr. Emily Black, and Dr. Paul Carter. We have reasons to believe they took your records and tissue samples." Donna and the Doctor paled considerably at the mention of the last two scientists.

"How d-did they escape," the Doctor asked, fear lacing his voice. The soldier shrugged his shoulders.

"We believe there were several escape exits that we didn't know about," the soldier said, "They either ran when we arrived or they escaped beforehand, deciding to go their own separate ways. Either way we can't find them." Jack nodded his head, tapping his chin and ruffling his hair in a nervous manner. He was hoping to catch them all, but that hope apparently was to big.

"Anything else," Jack asked.

"Yes, we'll be leaving for the campgrounds we set up in between the warehouses and forest in a couple hours, but first we need to blow up the Underground base. It has a deadly disease that needs to be immediately destroyed."

"What about the affected victims down there. You pulled them out didn't you," the Doctor asked. He glanced up at the soldier, desperation in his eyes.

"No, sir...Doctor," the soldier replied, "The team was too nervous about pulling them out since they're highly contagious. They're going to die along with the building.

"You're going to set them aflame," the Doctor snarled in anger, "They're people too you know and you're going to murder them in the most horrendous way possible."

"Sir...Doctor there was no other choice," the soldier stammered. The Doctor shot up off the floor and Donna and Jack immediately began fussing over him, telling him to lay back down. The Doctor pushed them away as he stared daggers at the young officer.

"There's always a choice," he chillingly answered, "I'm not going to allow anymore people to die."

"But Doctor they're going to die anyways," the soldier reasoned, "It's best to put them out their misery now." The Doctor stomped pass the young soldier, shoving him viciously out of the way.

"I don't reason with idiots," the Doctor bit back. He marched over to where the commanding officer was sitting. Donna, Jack, and Kurt trailing behind. He clutched his abdomen as it throbbed sorely, but he ignored it. He had a promise to keep.

"Doctor, as a medical professional I believe you straining yourself so soon will lead to damage in the muscle tissue of your abdomen," Kurt stated, "I believe you should relax."

"No," the Doctor responded coldly, "Not until I'm finish reasoning with the commanding officer. He's going to blow up a bloody building with innocent people inside. I don't believe it."

"But Doctor we have no way of curing them," Donna stated, "I completely disagree with the blowing them up part but when we get them out they'll suffer a slow and painful death. Do you really want that?"

"I'll find a way to cure them," the Doctor stated, "I have too. I promised." Donna's gaze softened as she nodded in understanding.

"Ok," she said, "I trust you. Just don't hurt yourself." Jack watched in concern as the Doctor approached Jameson. He was wobbly on his feet as he approached the brigadier.

"Are you Brigadier Jameson," he asked. Jameson turned his gaze to the pale looking Time Lord and a smile lit his face.

"Oh, Doctor it is an honor to meet you," Jameson said. He reached a hand out but the Doctor didn't take it and the smile dropped from Jameson's face. "What's wrong."

The Doctor glowered menacingly. "You're going to blow-up innocent people because they have a disease," the Doctor stated, "I do not approve of that."

Jameson rubbed his face and sighed. "Doctor, I understand you've been through a lot and you want to see everyone alive and well but these aliens are contagious. If they are ever released into the public, a lot of people will die."

"They don't need to be killed though," the Doctor stated, "I have a plan that doesn't deal with anymore bloodshed."

"And what is that plan," Jameson asked, "because at this moment I only see a whole lot of disastrous events if the plague carriers are released."

"Then don't release them," the Doctor stated, "give them to me. I can find a cure for them."

"By the time you find a cure for them, they'll be dead," Jameson argued, "You're just prolonging their misery."

"Humans," the Doctor muttered in exasperation, "They have no imagination."

"I believe I have an excellent imagination," Jameson sniped back, "and its pointing to a disaster waiting to happen and a group of aliens suffering a slow agonizing death." The two men glared at each other, before Jameson dropped his gaze. The alien's eyes were terrifying to gaze into for too long. He could see the darkness and power rumbling beneath.

"Does stasis chamber mean anything to you," the Doctor asked. Jameson widened his eyes and nodded his head.

"I can keep them dormant for as long as I need too," the Doctor stated, "They won't feel any pain and my TARDIS can run diagnostics on their diseases. I can verify the issue and find the cure without worrying about them dieing." Jameson scratched his chin before nodding his head.

"That could work,"he muttered. He glanced up at the Doctor and nodded his head, "Try it. I would like to avoid anymore deaths for the day." The Doctor smiled and shook Jameson's hand. "How do you plan on getting in there?"

"The TARDIS," the Doctor responded, "I know the old girl is exhausted but she might be willing to do one more jump before resting." The Doctor turned swiftly around with Donna, Jack, and Kurt following him.

"Jack I want you to make sure that no one detonates that building until I'm out," the Doctor ordered. Jack saluted playfully, before running towards the people with the firearms. "Kurt go back to your patients and prepare them for the ride back." Kurt nodded his head, taking a quick worried glance in the Doctor's direction before running back to the medical tent. "Donna." The Doctor turned around. "I want you to stay here and help around." Donna paused and crossed her arms, she glared at the Doctor.

"Not in a million years, spaceman," Donna retorted, "I'm not leaving your side again." The Doctor sighed.

"But Donna..." he did the familiar whine when he wasn't getting what he wanted. Donna almost smirked at that.

"No, I'm helping you and those poor aliens," Donna stubbornly stated. The Doctor ruffled the back of his head, giving up on arguing his point.

"Fine," the Doctor said, "We just have to move quickly though." Donna nodded her head and the Doctor clicked his fingers. The TARDIS doors swung open and the two friends stepped inside. Donna breathed a sigh of relief.

"Hello old girl," she stated. She ran her fingers lovingly over the wall and heard the ship purr with delight. "How have you been?" The TARDIS immediately darkened and a puff of cold air brushed the two passengers face as the old girl hummed with anger.

"Oh, I know," Donna responded, "I feel the same way." The Doctor had walked over to the console, leaning his hands among the buttons and levers. He closed his eyes as he took several deep breaths.

"Please old girl," the Doctor begged, "just a couple more jumps and we can rest for a couple days before taking the others home." The TARDIS immediately switched on a few buttons as she started her engines, she helped her pilot move around the console and switched on the buttons he couldn't reach.

The TARDIS gently flew herself over to where the diseased aliens were, landing with a silent thump. The Doctor smiled and patted the console. He slowly made his way out of the TARDIS with Donna's help. The TARDIS clicked open her doors, trying to make the walk smoother for the Doctor.

He stepped out into the pathogen lab where he was met by ten or more startled faces. The Doctor limped out with a smile.

"Hello," the Doctor stated, his voice slightly strained, "I told you I'd be back."

"I thought I told you to leave," the alien he conversed with before stated. Her hair had turned a sickly blue and she laid sprawled on the floor.

"And I told you I was going to help," the Doctor retorted.

"We're diseased," she snapped, "We're going to die anyways. Why won't you let us die?"

"Because I'm sick of death," he snarled, "Now you better let me help you or else." The alien snapped her mouth shut and leaned against the far wall.

"I have a stasis chamber in my ship. That will stop your bodies from dieing as well as take away the pain," the Doctor explained, "I'm going to put you lot in there while I figure out a cure for the disease. It could takes weeks, maybe even years but you'll be sleeping the whole time and if I'm lucky. If I'm very lucky, I'll hopefully be able to find a cure." The aliens glanced among each other, none answering. "Oh, come on it's better then being blown to smithereens." Finally the female alien sighed, coughing violently.

"Fine," she said, "We'll take you up on you...ahem...ahem your offer." The Doctor turned to Donna and smiled and they went to unlock the cages.

* * *

Jack waited anxiously for the sound of the TARDIS. The soldiers wanted to blow the place up and forget about everything but Jack kept giving excuses of why they shouldn't. They believed they had a deadline even though Brigadier Jameson told them to wait. Jack sighed in relief as he heard the groaning wheezing sound of the TARDIS and a loud thunk as it materialized. He turned around to see the doors open and Donna step out.

"Did you save them," Jack asked. Donna nodded her head a grin on her face.

"They're all in stasis right now," she responded. Jack nodded his head before taking the detonator remote. He slammed his hand on the button and the whole Underground base blew up in explosion of fire and smoke. The building crumbled to the ground and was no more.

* * *

**Thank you for all the reviews! They made me really happy. I know the Doctor is jumping between being scared and cowering to instant hero, but his mind isn't in the right place at the moment. It is a jumble of thoughts and fears and he can't decide who he is anymore. Yes, he's still the time travelling hero we all know and love, but now he's also even more broken then previously. Well, anywho, only a few more chapters left until this story is over. But no worries there will be two stories based around the Doctor's healing. :) Thanks again!**


	45. Chapter 44

**Thank you so much for all the wonderful reviews! Here's the next chapter! Hope you enjoy!**

Chapter 44

Donna strode around the campground they had created between the forest and the warehouses. Tents were lined up and vehicles were parked one after the other. It was her and the Doctor's last day in 2015 and all the aliens were buzzing with excitement about going home. Donna sauntered over to the tent, that she, Jack, and the UNIT officers had used to plan the rescue mission. She heard a group of men, ranting loudly and found a van behind the tent. Donna knocked on the door and the door flew open revealing Jack.

"Hey I heard yelling," Donna stated. "what's going on?" Jack rubbed the back of his neck and summoned Donna in. Donna stepped into the van where six men stood around a little tv, all staring intently at the footage that was shown. Donna squeezed in between them, her eyes scanning the footage. The sound was on low, but she could definitely hear screaming. Her mouth widened when she recognized the ever familiar blue box with a group of men around the ship.

"I think you should see this," Jack said solemnly. A frown curved his face and he glanced sadly at the beloved ship. The footage was rewound and the sound turned up. Colonel Graham was standing to the side with his hands behind his back as several men maneuvered a giant drill aimed at the TARDIS doors. It shot bright lights of energy into her doors, trying to melt them away. Donna could hear the TARDIS wailing in distress. It was an extremely high-pitch screeching hum, but she would know the sound of agonizing pain anywhere. Donna covered her mouth in shock, tears trailing down her face. She had been doing a lot of crying lately and to see her favorite blue box in distress was too much.

"Are they torturing her," Donna asked the obvious. Of course they were torturing the TARDIS, that was obvious in the footage. "Is that what's causing her pain?"

Jack shook his head and pulled Donna close, rubbing a comforting hand up and down her arm. He hated seeing the wonderful time ship in pain too. She had grown on him, with all of her mischievous tricks and playful antics. He could honestly say the TARDIS was a friend even though she did not speak.

"No," Jack replied. "This is what's causing her pain." He zoomed up to a tiny metal box that was vibrating. A scientists was next to it, turning up the dial. Donna squinted her eyes as she glanced at the box. How could something so tiny cause so much agony to the ship?

"What is it?" Donna asked. The TARDIS wails grew louder as the dial was cranked.

"It's a time distorter," Jack replied. "It creates fake paradoxes and as we all know TARDISes are very time sensitive. That's why she ran to the end of the universe when she last saw me because I was wrong, a paradox, a fix point in time." Donna nodded her head, but did not answer. She didn't know what to say.

"The funny thing is," Jack continued. "these were used during the Time war. The Doctor told me about it and as a time agent, I learned a lot about the Time Lords since they were a bit of a legend at the academy. Never thought I would travel with one. But the time distorter was used to weaken battle TARDISes during the war. Everything about the TARDIS would collapse and malfunction allowing easy entrance or destruction to that TARDIS. It was also a torture mechanism. If you torture the TARDIS, you torture the pilot."

"But the Doctor didn't complain or scream in pain when she was being tortured," Donna stated. Bile rose up her throat at the realization. Maybe he was, but didn't let anyone know.

"Maybe the Old Girl was protecting him," Jack suggested, "Blocking their telepathic connection so he wouldn't suffer. She knew he was already suffering enough without adding in her own distress."

"It sounds like something she would do," Donna agreed.

"The TARDIS is stubborn and tough," Jack stated with a hint of admiration for the ship. "to be able to withstand such a high amount of time change is quite impressive. She didn't even crack her doors open." Donna nodded her head in agreement, watching the TARDIS in the footage. Her doors stayed clamped shut, no matter any of the attacks she received.

"It makes me admire her even more," Donna stated, turning to Jack. She lifted a curious brow. "But my question is how did the Underground receive such a rare piece of technology if it was in the Time Wars?" Jack shrugged, scratching the back of his head.

"That's what I'm trying to figure out," Jack stated. "Apparently the Colonel had a supporter from some different century, maybe even someone from the time wars."

"Somebody who would've know about the Doctor's existence and survival," Donna added. "And would've known how to stop him. But why would they of wanted to turn the Doctor into a weapon or supported a group of people who thrived in torturing aliens?" Jack shrugged. The new revelation the footage had provided only caused more questions then answers.

"The Doctor's a dangerous man," Jack stated, "And if someone was able to gain full control of him, he could destroy whole planets with a snap of his fingers."

"But maybe it's not only weapons this mystery person wants," Jack stated. "Time Lords hold a lot of artron energy in their bodies since the planet,Gallifrey, was built on a time rift. That's why they have a longer life span then most sentient beings. But all that energy in one body could power a whole city for years as well as a large ship."

"So this means this mystery person had either taken part in the time war," Donna concluded. "Or like you, he or she is a time agent, who knows a lot about the Time Lord legend."

"Or is somebody else completely," Jack added.

"But they have to be from the future to give the Underground such a valuable piece of tech," Donna replied. The other six men in the room had stayed quiet the whole time as they listened to the two companions try to put the mystery together.

"Maybe this person was using the Underground," one of the men suggested. "As a storage unit for the Doctor, before he or she could collect him. They were using the Underground to break his spirit as well as learn about the Doctor in the process."

"Or they were working together," another man stated. Donna shrugged her shoulders, tapping her chin in contemplation.

"I don't know, but we need to find out," Donna stated. "Do you think that's why the four scientists ran off because they were working with this mystery person. Maybe Colonel Graham had no idea who this person was because he was pretty anti-alien. He just accepted the different torture devices without question."

"All pawns in one giant sick game," Jack replied. Donna nodded her head in disgust. She turned away from the footage and glanced at Jack.

"Hey Jack," Donna stated. "I'm going to find Spaceman. See how he's doing." Jack nodded his head as he rewound the feed.

"Alright, tell him Jack said hi," Jack replied. Donna nodded her head. As soon as they had returned to the campground, the Doctor had locked himself in the TARDIS, refusing to come out. Only Donna was allowed entry. He had sat in the captain seat, his face blank and Donna knew it was some sort of coping mechanism. But she also knew he had to talk at some point because bottling stuff up like this was dangerous to his sanity and health. Donna solemnly stepped out of the van and headed towards the blue box that stood tall in the middle of the camp.

* * *

Ama leaned against the TARDIS's blue wall, Ama's ear pressed against her. Ama's eyes were dilated and distant and her face was straight. No emotion was present on her young blue face.

"Hey Ama," Donna asked, "What are you doing?"

"She's sad," Ama mumbled distantly, "So worried for her thief. She feels his pain, but he can't feel hers. She doesn't want him to suffer anymore. Poor, poor Old Girl, you will be better soon. Her heart aches from the sickness that they caused her, but she wants to get everyone home. She has to get everyone home."

"Ama," Donna asked again, placing a hand on the girl's shoulder. "Are you alright?"

"Donna," Ama stated. "Great danger is promised in the future. You must protect your little boy." Donna stared blankly at Ama, she didn't even know what that meant. What little boy? Ama suddenly shivered and her eyes shrunk back to normal size. She gave a heavy gasp before blinking her eyes rapidly.

"Hey Donna," she said with a shy smile. "When did you get here?" Donna stared at her, mouth gaping.

"What the hell was that," Donna asked.

"What was what," Ama asked confused. Her nose scrunched up in contemplation. "I don't understand?"

"All that nonsense you just spouted," Donna replied. "All the great danger in the future and stuff." Ama shook her head confused.

"I don't know what you're talking about," Ama responded. She turned away from Donna and sauntered in the other direction. "I'm going to alert Roc and the others that we're leaving soon. We'll be waiting outside." Donna nodded her head, her blue orbs holding the confusion she felt before she turned into the TARDIS, plastering a smile on her face.

* * *

The Doctor was leaning against the console in concentration, he did not look when the TARDIS door creaked as Donna entered.

"Hey, Spaceman," she said cheerfully. "What are you doing?" The Doctor did not turn around. He only closed his eyes and breathed deeply.

"She won't talk to me Donna," he responded, frustration evident in his voice. "She talked to me once, called my name but now she won't do it. She only sends me her emotions instead of actually physically talking inside my head."

"Doctor, you said yourself, the TARDIS can't physically speak to you," Donna stated. "Maybe you were..."

"No! I wasn't imagining things," the Doctor answered sharply. "She called my name but now won't do it again. I don't know why she did it, she never does, and now she won't show me the reassurance she did before." He kicked the side of the TARDIS console, hissing in pain as he stubbed his toe. The TARDIS hummed angrily at his flaring temper, the lights turning a dark red. "Why won't you talk to me!"

"Doctor stop it," Donna snapped. She marched over and grabbed his arm, forcing him to sit down. She had never seen him react so violently with anyone and that scared her. "Do not yell at her. If the TARDIS did talk to you, she had her reasons. Were you depressed and injured?" The Doctor nodded his head, rubbing his arms in comfort. Donna sighed, closing her eyes. She knew, when they got back home, she would have to help him control his temper. It was irregular and random and she never knew what was going to set him off. She was worried he was suffering from brain damage of some sort, thanks to how many times he was kicked in the head or violently thrown against the wall. She would have to talk to a doctor, see if his rapid mood swings was the cause of head trauma and/or post traumatic stress disorder. She needed to get him into a quiet environment and fast.

"Maybe that's why she talked to you," Donna stated, "Maybe she was concern and knew you needed to hear her voice, so you could pull yourself out of your guilt." The Doctor shrugged. He was clad in his normal brown pinstripe suit, but refused to wear shoes for some odd reason that Donna didn't know why. Maybe another side-affect to the trauma, he's suffering from.

"Maybe," he mumbled. He leaned his head on her shoulder, sighing deeply. He ran his fingers against the buttons, initiating a pleasant purr from the Old Girl. "I'm sorry I loss my temper." the TARDIS vibrated under his touch. Donna ran her fingers through his hair, smiling slightly as he sighed deeply.

"Feel better," she asked. He nodded his head, yawning. "Alright. I'm going to say bye to everyone and then we can take the aliens home." She patted him on the shoulder as he lifted his head from her shoulder.

"Donna after the aliens," the Doctor said, "I have a couple of stops I need to make. The TARDIS agreed with me, when I suggested it. It's sort of closure for me and her. Would that be alright with you before we relax and everything?" Donna nodded her head, a soft smile on her lips. Yep, Spaceman was going to be alright. He just needed a little help, heading in the right direction of healing and she was going to be there for him no matter what.

"Of course Spaceman," Donna answered."I'm alright with that. Whatever you need." The Doctor nodded his head, chewing his lip. Donna was about to turn out the door when the Doctor stopped her again.

"Donna," the Doctor asked. She turned back around to face the Doctor. He looked at her, embarrassed and guilt-ridden. He glanced down at his bare toes shyly.

"Yeah," Donna replied. She crossed her arms, waiting for the question or comment. Whatever he needed to say.

"Donna I would never hurt you," the Doctor said. "I know I'm different and I feel different. But I want you to know I would never hurt you." He sniffed, rubbing at his eyes. "You do know that right?" Donna softly smiled and nodded her head.

"Yeah, I know that Spaceman," she responded. "I trust you." The Doctor gave a sigh of relief as he leaned back into the captain's seat. Donna smiled.

"I'll see you in a few minutes spaceman," she said. "Don't panic when the TARDIS is crowded. Everyone coming with us, just wants to go home. Alright?" The Doctor bobbed his head, fiddling with the buttons. Yeah, he was going to get better. She just knew it. She stepped outside of the TARDIS, her thoughts racing as she was greeted by a crowd of aliens, all waiting to go home.

"Alright, everyone," she said. "Have you made your goodbyes." The aliens nodded, staring skeptically at the blue box. She chuckled, knowing exactly what they were thinking. "Alright go on in. we'll be leaving soon enough." The aliens nodded and stepped into the TARDIS. Donna could hear the gasps of amazement and wonder as they walked into the bigger on the inside ship. She could hear the TARDIS vibrating with delight as the alien passengers complimented her interior. Donna turned back around at the sorrowed face Torchwood team.

"Hey turn those frowns upside down," she exclaimed. "You'll be seeing us again." She hugged each member of the team. Kurt gave a warm friendly hug, wishing her good luck. Diane kissed her on the cheek, telling her how much she was going to miss her. Johnny did a half hug and a grunt, before turning away. While Becky enthusiastically threw her arms around Donna's neck, saying how much she was going to miss her. Donna hugged them all before Jack dipped down, pulling Donna close and whispering in her ear.

"See you in the past," he said cheekily, giving her a playful wink. Donna smiled.

"Yeah see ya," she responded before punching him in the arm. "Captain flirts-a-lot." Jack laughed before waving a goodbye.

Becky hugged her once more and Donna couldn't help but notice the fob watch entwined between Becky's fingers.

"Hey Becky where did you get that watch," Donna asked. Becky glanced down at the watch as if noticing it for the first time. She shrugged her shoulders.

"Don't know. I've had it forever," Becky responded. "It doesn't work properly though. It's broken." Donna nodded her head a curious look on her face before waving goodbye. "Bye Donna!" Becky shouted. "Hope to see you soon!"

She stepped into the TARDIS and the Torchwood team waved as the ship dematerialized.

* * *

Becky pocketed the watch, stepping away from the crew and sauntered off towards the vehicle they were leaving in. The rest of the team soon followed, picking up their things and preparing for the long drive back to the Torchwood base. Jack stared at the place where the TARDIS used to sit. A sad smile appearing on his lips, He sighed deeply.

A UNIT soldier stepped forward to Jack, his arms behind his back and head raised.

"Captain Harkness, sir," the Soldier exclaimed. "I have information concerning Dr. Jane Morley, sir." Jack nodded his head in a gesture to proceed.

"She has been given bail and released from the UNIT jail under the careful guidance of her lawyer," the soldier said. "She has claimed she had not hurt the aliens once and should not be carted away like a felonious criminal."

"But she was there," Jack exclaimed. "and because of that, she made sure the Doctor was imprisoned and hurt."

"Yes, but sir," the Soldier continued. "She had no part in the creation of the virus or the serum. We can not charge her, do to the laws. Basically she's innocent. She was only there to perform her psychology studies on the aliens." Jack's face reddened with anger at the injustice of this time period.

"But she hurt the Doctor," Jack argued. "She allowed those monsters to cause physical harm to him."

"But she did not hurt him directly," the Soldier responded, "It was proven in the video footage. This means Dr. Morley is a free woman." Jack nodded his head, scratching the back of his neck.

"Damn,"Jack stated. He rubbed his eyes in frustration. "Fine. I can't argue with you lot. This is just unfair. How many more people will you pardon!"

"It's up to the court, sir," the Soldier said. "I have no say in this." Jack nodded his head and turned away.

"Fine," Jack stated. "You may go. I'm going home." He turned away and headed back to the van,muttering to himself. The soldier saluted and marched the other way.

* * *

**I hope you enjoyed that chapter. :) Only three more left before this story ends. Please review and tell me what you think. :)**


	46. Chapter 45

**Thanks for all the wonderful reviews. I'm glad you enjoyed the chapter! :) Here's the next chapter! Tell me what you think! **

Chapter 45

The Doctor took each alien to their home planet. He watched as Ama ran to her parents, throwing her arms around their necks, and weeping her eyes out as her little brother hugged her from behind. He watched a Roc was tackled by his many brothers and sisters all chattering with excitement at seeing his return. He watched Tak hug his grandmother with a tearful smile as she hummed comforting lullabies to her grandson. He watched the slitheen slowly move over to her extended family, each member greeting her in their own fashion.

As the Doctor stopped at each planet, he watched each alien get a tearful, happy welcome from their aunts or uncles, mothers or fathers,brothers or sisters, grandfathers or grandmothers, or cousins and he couldn't help the horrible lump that formed in the back of his throat, choking him with sadness. He would never have that experience again. Of returning home to his planet and being welcomed by loving arms. It was gone and he was alone and he couldn't help the loneliness that darkened his soul and made him feel ill. A tear slid down his face as he watched the last person he dropped off. He would forever be an alien. He had no home to go back to. All he had was space, the stars, and his TARDIS. Every planet he had or ever will journey too would always consider him an alien.

The Doctor choked on a sob that clogged his throat. He was tired, so very tired and life just wore him down more everyday. He slumped against the console, his TARDIS once more empty. He was alone. He felt a soft hand touch his back and he glanced up with teary brown eyes. Donna stood there next to him, rubbing comforting circles on his back. Her eyes held nothing but compassion and devotion. He sniffed loudly, bowing his head as soft, warm, human arms wrapped around his torso. Ginger hair curtained his back as he felt Donna lean her head against him. He turned around to face her, lips wobbling with held back emotions and he fell into her arms. Tears streamed down his face as he cried into Donna's shoulder.

He curled up into her arms and she sat down on the captain's seat, holding him close as she whispered sweet,comforting words into his ear. He promised himself he wouldn't cry but watching everyone go back home to a family was just to much for the Time Lord. He couldn't help but think about the family he lost in the last great Time War. His brother and sister, his cousins, his aunts and uncles, his wife and children. Everyone just gone. He had no family to go back to. No family to help him heal or comfort him on those nights where he screamed in fear from the nightmarish memories that constantly bombarded his soul. No one of his own kind. He was completely and utterly alone.

"Why," he sobbed into Donna's shirt. He clutched at her blouse, curling up into her arms even more as another heavy gust of tears soaked Donna's shirt. Donna rocked him back and forth, shushing softly and biting her lips. She didn't want to start crying because if that happened he would stop and comfort her, instead of getting all of his feeling off his chest. He needed this moment to curse at the universe and wash away the ever building emotions. She wanted to be there for him and if it meant being the person he cried on, then so be it.

"I don't know sweetheart," Donna mumbled softly into his hair. "I just don't know." He clutched her tightly, rubbing his tear soaked face against her chest. She softly raked her fingers through his brown hair.

"Why does the universe hate me," the Doctor muttered as a hiccuped sob escaped his mouth and fresh tears flowed from his eyes. "Everyone I love is pulled cruelly away from me at some point and then I am once again alone." Donna shook her head, biting her lip. Soft water drops dotting her eyelashes as she forced back the tears.

"My family," the Doctor continued, "My planet...My...My..." He choked on the words as the hiccuped coughs came back and he threw his head back, howling in sorrow and pain. He fell back into Donna's arms, snuffling. "They're all gone and I am a-alone." Donna covered her mouth, her eyes had grown wet and her sight blurred from the tears that wished to spill.

"I'm so sorry Spaceman," she said. Her voice hiccuped. "I wish I could change everything." The Doctor glanced up, his eyes red and puffy from crying. Tear tracks trailed down his cheeks and he used his sleeve to wipe them off.

"Yeah," he agreed somberly, "Me too." Donna continued brushing his hair back with a soft hum.

"Spaceman,"Donna said. "I want you to know, I'm always here for you. Whenever you need comfort or someone to talk to, my doors are always open." The Doctor nodded his head, sighing. He snuggled closer into Donna's chest, enjoying the gentle touches that was denied to him for so long. "I know I can never replace your family or your people," Donna continued. "They'll always have a special place in your hearts. But I'll be happy to be whatever family figure you want me to be because your my best mate and I hate to see you sad."

The Doctor glanced up at her, a sincere smile forming on his face. His thumb stroke away the tear that slid down her cheek. She sniffed stubbornly, wiping at her eyes.

"I promised myself I wouldn't cry," she stated. The Doctor chuckled quietly, leaning back into her embrace.

"Oh, Donna Noble you are brilliant," he said. His voice full of honesty at the statement.

"Oh, shut-up you," Donna responded, giving him a loving pat on the back. The Doctor laughed, cuddling closer.

"You know you're really warm," he stated with a purr. "My soft, warm human."

"Spaceman, you start calling me that people are going to give you looks and question your sanity," Donna retorted playfully.

"My sanity's already questionable," he mumbled sadly. Donna's face automatically dropped into compassion.

"I'm sorry spaceman," Donna replied. "I promise you it will get better soon."

"That's what everyone keeps saying," he retorted, "But when, Donna, when will it get better? I'm sick and tired of people saying that and nothing ever changes. It's depressing and life only seems to get worse." Donna glanced down, the Doctor's head buried under her chin.

"I'll make it better. I promise," Donna responded. The Doctor scrunched his eyebrows, a frown appearing on her face.

"Don't make promises you can't keep," the Doctor muttered.

"I promised forever, didn't I," Donna argued. The Doctor shot up, fire blazing in his eyes. He stomped over to the console, leaning against it as the weight of the universe rested on his shoulders.

"Your human Donna," he explained, "You wither and you die while I live on, never stopping, never growing old. Just changing." He turned back around, staring Donna in the eyes. "I can't watch that happen to you. I just can't." He sniffed and rubbed at his nose. "I can't see you die and disappear just like Bobby." Donna's face softened and she approached the Doctor once more.

"I know, but we will find a way for it to work, alright," Donna replied. The Doctor nodded his head, holding his chin high. He wiped away the tears and turned back to the console.

"I have two stops I need to make," the Doctor stated, "Before we relax." Donna nodded her head, placing a consoling hand on his back.

"Alright," Donna responded. The Doctor pulled one of the TARDIS levers with lack of enthusiasm. The TARDIS lurched into sudden movement as it flew through time and space. The Doctor held onto the rail, the gleeful laughter did not exit his mouth like it once did.

* * *

_Couple hours after the first Underground escape:_

The escape alarms had just turned off, telling everyone that the escaped prisoner had been captured but Claire still heard the loud clomps of military boots outside her door. She had returned back to her medical office as soon as the alarms were silenced, sauntering over to her desk. She leaned against her desk, her head resting in her hands. Her mind kept on wandering to the alien that tried to escape. Those big, brown eyes pleading her to help. That smile had melted her heart as soon as he flashed it and she couldn't help but hope that he did escape. He was clever and she liked clever, he had a way of being witty and quick in the face of danger and she loved it. Claire smacked herself in the face.

"Get a grip Claire," she reprimanded herself. "You're falling for an alien that you only met three times." And she had only met him three times, but the first two times he was injured with blood gushing from his wounds.

Claire sighed, resting her forehead against the wooden desk. Now he was captured once more and probably being tortured while she sulked. She really hated her life right now. Why did she ever except the job offer to begin with? She could of used her medical skills for the better instead of stitching up abused aliens, so they could be cut open and tortured once more. She propped her elbow on the desk, resting her head in her hands.

The Doctor...that's what the alien was named. It was a strange name but it suited him. He had a gentleness about him, a gentleness not meant to be here and she feared that the Underground would change him. Claire let out another groan. She should run like he told her too. She was not meant to be in a place like this. But where would she go? She had no where and the Underground made sure of it. Her family was long gone and she never considered starting a romantic relationship because of her _job_ and she knew if she ran, they would find her and that would be the end of Claire Michaels.

Claire brushed back her raven black hair. No one ever got out alive when they were part of the Underground. She wished she had been wiser in her job choosing but then again she would of never met the Doctor, who was surprisingly very attractive...for an alien.

Who was she kidding? She had no one and her only chance she had of escaping was chained up in some room being tortured by the idiots who ran this place. Claire folded her arms on the desk and buried her face into the crook of her arm. She was just going to rest her eyes for a while and forget about how awful she felt. She wanted to take the Doctor to the exit but he was too stubborn and she didn't even know what he was looking for. Claire sighed heavily, one green eye peaking out towards the cabinets that held her medical equipment. If only she had a way to leave, that was her greatest wish.

Claire perked up as she heard a loud, groaning wheezing noise and wind picked up in her office as papers flew in all directions. She jumped up, stumbling away in shock as something blue began to materialize in the room. What the hell? With a loud thunk, a blue box stood tall in the middle of her office and she couldn't help the shock expression that graced her face. She placed a hand on her heart, heaving deeply before curiosity finally took over. She cautiously stepped over to the blue box and placed a hand on the wall. It vibrated under her touch and she jumped back in surprise. The door to the box snapped open and bright light shone out from the doorway as a tall man stepped out of the doors.

Claire's green eyes widened in shock and she pointed at the tall man as if seeing a ghost.

"But...you're," Claire stuttered. "You were...I saw them..." She never had been so confused in her life. How could the Doctor be standing right there when she saw him get dragged off to the room minutes ago. Her head felt ready to blow-up in a million trillion pieces, thanks to all the confusion she felt. The Doctor sighed and stepped closer. His brown hair was wild and ruffled and his brown pinstripe suit...which she had not seen him wear before...was rumpled. He rubbed the back of his neck awkwardly.

"Yes, quite right," the Doctor stated, "I should probably explain myself." Claire glared at him sharply, she wasn't angry just extremely confused and wishing she knew what was going on.

"Ya think," she retorted. "I just saw you get carted off a while back and now you're standing in front of me, dressed nicely and unbruised. What the hell is going on? Did they take a hologram you or something while you made your clever escape?" Her mind was spinning with all the confusion and possibilities. The Doctor snorted in laughter at the thought.

"Holograms?" The Doctor responded, "Don't be ridiculous. You can't physically touch holograms until the 53rd century and that's only because some scientist got lucky when accidentally messing up the original formula." Claire stared blankly at him. She had nothing to say but to confirm her original beliefs that he was mad. He glanced down sheepishly for a second as he caught her look.

"Yes, right. How I escaped," He stated. The Doctor took a deep breath. "I'm from the future."

"Get out of here," she responded. She rolled her eyes, blowing the bangs out of her face.

"No seriously I am," he exclaimed, "I just escaped a few days ago with the help of my friends."

"But you're down in the interrogation room," Claire stated, trying to understand the illogical statement.

"Well, yes my past self. That self hasn't escaped yet," the Doctor stated, before pointing to himself. "While this self has. It...It's wibbly wobbly timey wimey stuff." Claire just shook her head and threw up her hands in surrender.

"Whatever," she exclaimed exasperated. "Don't tell me." She stomped over to her desk and started looking through the papers on her desk. She really wasn't looking for anything just releasing her anger. The Doctor...though he was an alien...responded in the typical bloke fashion and she was sick of it.

"No, I did tell you Claire," he responded before scrunching his eyebrows. "Just not clearly."

"Do you mind explaining it to me clearly," she snapped back. The Doctor scratched the back of his neck.

"I'm a time traveler," he decided on. "I travel through time and space and I came here to take you away. To find a place where you can feel safe and enjoy helping people. Will you take me up on my offer?" Claire smiled. He did remember his promise. She couldn't help the blush that pinked her cheeks as she stared into those hopeful eyes. She chewed on her fingernail for a second before nodding her head.

"Alright," she responded. The grin that lit his face made her smile widen and he threw out his hand.

"Allons-y Claire," he exclaimed. He wiggled his fingers, smiling and Claire blushed, grabbing his hand. He led her towards the blue box and she couldn't help the doubting look on her face. It was going to be a tight squeeze in his ship, especially when a ginger popped her head out.

"Are you two coming," the ginger huffed. "I'm getting tired of waiting around, martian boy." The Doctor rolled his eyes, releasing Claire's hand, and stepped over to the door.

"Donna," he simply stated as he stepped into the box. The woman, apparently Donna, smiled cheekily and disappeared back inside the box. Great, three people in one tiny box. Hope the ride doesn't take to long. Claire steadily climbed into the box. The doors slammed shut and the loud groaning was heard as the TARDIS dematerialized. A gust of wind was the last to settle.

The knob to Claire's office turned as the door creaked open. Dr. Morley stepped in, glancing around the room, papers were strewn all over and there was a slight breeze in the normally stagnant room. Dr. Morley's lab coat swished as she entered the office.

"Claire," she called, "Claire, where are you dear?" She glanced around the empty room, dread clutching her heart. Had there been a fight? Had one of the aliens escaped and killed the young medic? But that would be ridiculous, some of the aliens had already been captured while the others were gone, disappeared into the night. Dr. Morley sighed. She must of ranaway. Dr. Morley couldn't help the smile that curved her lips.

"Good for you Claire," she whispered. She wouldn't bring it up with the Colonel right away instead allowing the girl a head start before they found out. She glanced around the room. The room had an eerie, supernatural feel to it. Like something was watching her. It wasn't the first time Dr. Morley got this feeling but every time it sent shivers up her spine and goosebumps down her arms. Something was always watching her. She glanced over towards a corner of the room and her eyes dilated as she stared at the darkened space. Dr. Morley felt a shiver run up her spine and she had the sudden urge to run. She didn't know why but she had too. Dr. Morley turned out the door, closing it with a slam behind her. When Morley was gone a dark cloaked figure materialized from the shadows. He flitted across the room like an apparition, before stopping at where the TARDIS had disappeared.

"Time Lord," It stated in a raspy voice. It sniffed deeply before standing to its feet and disappearing in a flash of smoke. The room once more empty.

* * *

Claire stared in wonder at the bigger on the inside ship. Her eyes were the size of saucers as she observed the magnificent architecture of the beautiful time ship. The ship looked like it was organic with coral beams that reached the ceiling that seemed to go on forever. The console stood in the middle of the room with a green pulsing tube in the middle of it. The Doctor and Donna leaned against the railings, smiling at her response but she couldn't help but notice the worried glances that Donna kept passing at the Doctor. Claire stepped closer to the console and placed a hand on the buttons. There was a humming purr and Claire lifted her hand in surprise, a soft smile graced her lips.

"It's beautiful," she stated. The Doctor turned away from her, pressing a few buttons.

"She's beautiful," he corrected. "She's alive." Claire's eyes widened in shock at the revelation.

"A living bigger on the inside time box," Claire muttered, "Never thought I'd say that." Donna laughed and patted the girl on the back.

"Me too, sweetheart," Donna stated, "Me too." The Doctor spun back around, facing the two women.

"Alright Claire," the Doctor exclaimed. "I can take you anywhere or anywhen you want. I will leave you there and you can start a new life. Unless you have..." Claire shook her head.

"No, I'm alone. My family died long ago," she said sadly.

The Doctor glanced down, turning a knob. "I'm sorry for your loss,"he replied somberly. Claire shrugged, waving him off as no concern.

"No matter. It happened long ago," she responded. "So where do you want to take me."

"Your choice," the Doctor sing-songed. "If you're going to live there you better want it. Past, future, or another planet. Your pick." Claire raised an eyebrow, before crossing her arms.

"I think the future," she stated, "Past is too old fashion and another planet, I just wouldn't fit." The Doctor hit a few knobs and danced around the console.

"Alrighty then," the Doctor exclaimed. "Now for the time period. What shall it be?"

"Far away from this one," she muttered. The Doctor nodded his head rapidly.

"Yes, Claire do you mind being a little more specific," the Doctor asked, "Because I can take you to the 25th century, oh no rubbish place. Polluted air and people lived on floating ships to escape the polluted earth. What about 32nd century. Earth expedition made contact with a colony descended from Utnapishtim and refugees from Anu. Great medical advancements too. Absolutely spectacular. Or maybe you would like to head down to the 51st century. That's the century that my friend Jack's from. There's time agents, though maybe that was shut down after the first expedition. Oh, love! Love is a big thing in that century. Everyone loves each other and I mean quite literally. I got invited to bedrooms to many times to count when I was visiting. Which was actually really awkward...I think we'll skip 51st century." Claire just stared at the strange alien as he continued his ramble. She glanced over at Donna, who rolled her eyes and did the 'crazy' signal before pointing at the Doctor. Claire giggled.

"I saw that Ms. Noble," the Doctor stated without even glancing at the two women. He continued his ramble about New Earth in new new(13 more news) york and how the medicine and the medical staff was spectacular there, except when he visited with Rose. That wasn't a great day. Claire decided to interrupt his ramble since they weren't getting anywhere.

"How about you just take me to the century, you deem the best. The most peaceful place you can think of," she said. The Doctor glanced over as a smile curved his lips. "And it doesn't even have to be on Earth."

"I think I've got just the place," the Doctor said, "I can introduce you to my friend who lives there and he can get you a job." Claire nodded her head, heaving a sigh of relief as the Doctor put the TARDIS in motion.

* * *

Claire's eyes widened as she found herself on a planet in a futuristic century. Cars flew overhead and people walked along the streets in weird alien outfits. There were aliens and humans alike of all different shapes and sizes. Tall buildings lined the streets and restaurants with different cultural foods lined the road. The buildings flashed different colors and children ran across the street. There was no violent protesting, everyone seemed at peace.

"What is this place," Claire breathed in admiration.

"Halcya. One of the most tranquil planets in the universe," The Doctor responded. "This I believe is in the 42nd century. Earth is not a pretty place to live in since you humans destroyed it with all your cars and factories but Halcya does not use materials that cause pollution." The Doctor took a long sniff before sighing with content. "Smell that air, now that is fresh." Donna strode out, glancing at the beautiful architecture.

"Spaceman," she exclaimed in wonder. "This place is absolutely gorgeous!" The Doctor smiled and Donna grinned back. It was nice seeing him so relaxed, even if it was short lived.

"Well come on," he responded, "I have to go find Hammon. He's going to get you a job, Claire, and possibly provide you a place to live, just until you get back on your feet."

"Lead the way Doctor,"Claire replied. She knew she was going to love it here. She just knew it.

* * *

The Doctor and Donna headed back to the TARDIS after their quick meeting with Hammon. Hammon was a native to Halcya and was an extremely wealthy man. But all that wealth he gained was sent to building and supporting schools and people who were not as lucky as others. Though in Halcya, money problems was not a huge issue on the peace-loving planet. The Doctor stepped into the TARDIS, sighing deeply. It was good seeing Claire get along with Hammon so well and he knew Hammon would take excellent care of her. She was going to be fine. Her life would start on a clean slate and she'd be able to do the things she couldn't do before.

The Doctor fell into the Captain's seat, rubbing his eyes. Donna laid a comforting hand on his shoulder, Massaging his stiff neck. It was hard pretending to be happy when in fact deep down inside he felt miserable and broken. He just didn't want Claire to see him sad. Donna kissed him on the cheek, a comforting smile on her lips.

"Spaceman, we don't have to make the second trip today," she stated. "We can wait a bit. Let you and the TARDIS heal." The Doctor shook his head, pinching the bridge of his nose.

"I've got to Donna," he replied, "I need closure and this trip will provide that." Donna nodded her head, resting her arms at her side.

"Alright," she said, "Do what you need to do." The Doctor slowly got up, murmuring softly to the TARDIS. He flipped a few switches and the TARDIS hummed encouragingly to her pilot. The TARDIS jerked into action and immediately begin spinning through the vortex to the next destination. The Doctor leaned over the console, gripping the railing tightly as he held himself up.

* * *

**I hope you enjoyed that chapter. Two more chapters left and on the last one I'll tell you what the next story will be about. Keep reviewing! I love reviews.**


	47. Chapter 46

**Thanks for all the reviews! Well, here's the next chapter. :) Hope you enjoy. **

Chapter 46

The wind picked up in a slummy neighborhood in Birmingham. Newspapers tumbled down the streets as a police vehicle drove by, sirens blaring. Red bricked apartments stood side by side along the street and graffiti covered the walls. People bounced by, listening to music or talking with friends or neighbors. The chattering seemed to halt when a loud whirring noise echoed throughout the street and a blue box began to materialize out of thin air.

It was not uncommon to see strange and unexplainable phenomenons happen in this small neighborhood. Many times the streets were littered with gang violence and gunshots throughout the night or the sound of a howling wolf. Sometimes bright lights would flash across the neighborhood and extra-terrestrial beings would suddenly appear out of nowhere. But then again this was 2015 and aliens appearing was not that big of a deal since it seemed to happen a lot. With anti-alien protest constantly occurring on the streets, the neighborhood didn't understand why there were still a constant flow of alien encounters, considering all the hate that was spouted about their kind. But the neighborhood didn't care. It was the day to day life here and sometimes these little encounters made life a bit more interesting.

They watched as the blue box became solid and with a giant thump, all the whirring and wheezing had ended. Silence now surrounded the box. The locals sat there watching as the doors to the box slowly creaked open and a man shuffled slowly out through the door. It wasn't the black eyed, green alien they all thought would appear because whoever this was looked like a typical human man except for the fact he arrived in a blue box. The man shoved his hands into his coat pocket, glancing down at the ground. He was bare foot and no one knew why but they assumed it must have been some weird alien habit.

He glanced over at them his brown eyes capturing their gazes, he sighed heavily. They couldn't help but feel sorry for the strange man and as they looked into those brown eyes all they could see was hardship and betrayal written clearly on his face. He wanted them to see it and the people on the streets couldn't help but feel guilty as if they played a part in the man's misery. One girl, who sat on the stairs to her apartment, squirmed uncomfortably as the man...or alien considering how he arrived...seemed to stare deep into their souls, finding all their memories and actual feelings. The gaze scared them but they wouldn't dare move. The door creaked open once more and a ginger stepped out. Her hair was tied in a ponytail and she somberly walked over, grabbing the man's hand and squeezing it comfortingly.

"Are you ready for this," she asked the man quietly. The man nodded his head, sighing deeply once more as his free hand rubbed his red, puffy eyes where unshed tears sat stubbornly at the rim of his eyes.

"I need closure," he said. The alien-man drifted slowly towards the residences of the neighborhood and the people held their breaths expecting an attack. What else would you expect from an alien?

"Excuse me you lot," the alien-man asked, he glanced nervously over at the woman before lowering his head. "Do you know where Bobby Mills used to live?" One of the girls stepped forward, bubblegum in her mouth. She chewed loudly, placing her hands on her hips.

"Yeah we know where Bobby used to live," She drawled out, "But he's dead. So what's it to ya?" The man glanced down sadly, his mouth cracking open slightly as if to speak before closing. He glanced over at the ginger once more before turning back to the girl chewing bubblegum.

"Did he live with anyone?" he asked. The girl nodded her head, crossing her arms.

"Yeah," she said, "His mum." The man nodded his head, shoving his hands into his pocket.

"Is she here right now," he asked. The girl bobbed her head, popping the bubble she was blowing.

"Yeah, never leaves the house," she stated, "Bobby took care of her. That's why he gotta job as a janitor. Only thing he's good at anyways."

The man glanced up, his eyes cold with anger at the girl's quip. "No, Bobby was good at a lot of things. You just didn't know about them." The girl backed away, surprised by the sudden change in his demeanor.

"How did you know Bobby," she asked. The man's eyes softened once more and a sad smile curved his lips. He ruffled his hair slightly in reminiscence.

"He was a friend," he said quietly. "A really good friend." The girl nodded her head, before pointing a finger to the right.

"Bobby's mother lives four doors down on the first floor," the girl said, "Her apartment number is 106. She's sort of a hermit, so don't be too upset if she doesn't answer. She's had a rough time ever since she lost Bobby." The man nodded his head and smiled in thanks. He turned around, waving to the girl and the group of people on the steps of one of the apartment buildings before sauntering over to the ginger woman. The woman once again squeezed his hand in comfort before the two headed towards the apartment building. The group of residence watched sadly as the two walked away from the blue box that sat on the other side of the street.

* * *

The Doctor stopped at apartment 106, Donna right behind him. He quickly knocked on the door before nervously bouncing on the balls of his feet. Donna placed a hand on his shoulder, halting the nervous energy. She was just as nervous as him but unlike him, she wasn't the scapegoat to Bobby's murder. They had no idea how the woman would react but for both of their sake, she hoped the elderly woman welcomed them in. The Doctor needed to talk to someone who was close to Bobby.

The Doctor knocked on the door once more. He glanced around nervously, eyes landing on the neighbors that were watching them from across the street. He smiled shyly before turning back to the door. He was about to knock once more when he heard the door open. He stepped back as a little old lady glared at him. A cigarette hung from her mouth and her cheeks and eyes were hollow from the effects of not being outside in a while. Her gray thin hair was tied in a loose bun with strings of hair hanging around her face. The old woman plucked the cigarette out of her mouth, blowing smoke into the Doctor and Donna's face. The Doctor coughed as the smoke entered his lungs.

"What," the woman said sharply, "Haven't I told you lot before I don't buy anything you sell. Get off my doorstep!" She was about to slam the door when Donna threw her foot out and stopped the door from closing. The elderly woman glared at Donna, huffing angrily before a coughing fit took over. She doubled over as the coughs wracked her body. Donna immediately went over to check if the woman was ok.

"I'm alright," she grouched, slapping Donna's hand away. "I don't need any help from a salesperson." Donna backed away, raising her hands in a defensive motion. There were times when you argued and there were times when you backed away slowly and let things be. "I want you two off my property this instant or I'm calling the police."

"But Ms. Mills," the Doctor interrupted. "I'm here to speak to you about Bobby." The elderly woman's face automatically softened at the mention of her son.

"What about him," she asked somberly, she wiped at her eyes, dropping her cigarette. She stomped it out before kicking it into the bushes. The Doctor rubbed the back of his neck, glancing over at Donna, silently asking for assistance.

"He was a friend of ours," Donna replied, a sad smile crossed her face. "We used to play games together and talk and the Doctor over there." Donna pointed at the Doctor. "Taught him how to make origamis." The old woman raised an eyebrow.

"The Doctor," she raspily stated, another onslaught of coughs attacked her. She banged a fist on her chest, heaving deeply. "Bobby used to talk about a friend named the Doctor when he came home." She smiled softly at the memory of her son before wiping away tears. "He told me so many wonderful stories about you. He'd run at the mouth, telling me all the things you taught him to do." The old woman sniffed, wiping another tear away. "He looked up to you, Doctor. He never looked up to anyone to the extent that he did you." The Doctor bowed his head and Donna wrapped a loving arm around his shoulders. The old woman wiped her hands on her apron, looking at the couple that stood in front of her.

"Come on in," she stated, "I'll make you a cuppa." She turned away, slowly walking back into her house. Donna and the Doctor followed her in.

The apartment was tiny with two small bedrooms and a bathroom and a little kitchenette connected to a tiny living room. Dust covered every surface of the house and it was shadowed in darkness from the drawn curtains. A small tv stood in the corner of the room with a buzzing noise coming from it. Trash was packed int every corner and knickknacks covered every shelf. A fat black cat lounged on the tattered couch, covering it in fur.

"Go on sit down," Ms. Mills said from the kitchenette. "I'll be with you shortly. Make yourselves at home." Donna shrugged and took the Doctor's hand and they both sat on the tattered old couch. The black cat hissed in annoyance before jumping off and moving over to the other brownish-red chair in the corner. The Doctor leaned his head on Donna's shoulder, taking in every detail. From what Bobby told of his life, he seemed to be happy. The Doctor just didn't expect a tiny, dirty apartment with a mother who smoked cigarettes and never left her home. The Doctor's eyes stopped on a picture of a younger Bobby smiling with his mom and a man, he presumed to be his uncle. The Doctor glanced away sadly. Another life he had ruined.

"Here we are," the little old woman said, "Three cuppas." She handed one to Donna and the Doctor, taking the third for herself. She lit another cigarette and began smoking once more. The Doctor took a steady sip of tea before placing it down on the raggedy coffee table.

"Thank you," he said solemnly. Ms. Mills hummed in response, puffing out more smoke. She coughed violently before taking a large sip from her tea.

"So," she stated, "You're the alien that Bobby always talked about." The Doctor nodded his head silently, his eyes gazing down somberly. Her chuckle was raspy and dry. "No offense but I thought you'd be green." The Doctor smirked before shaking his head.

"Nope, not green." He held out his hand to confirm his point. Ms. Mills nodded her head, taking another sip of her tea. Her eyes distant as if in the middle of a memory. She shook her head, bringing herself out of it.

"Sorry," she said. Donna glanced at the sadly thin elderly woman. She was petite and possibly once beautiful but years of hardship and growing old wore down on her and now she was the sickly old woman in front of them. "Bobby was a good boy," she stated, "Always willing to help and bring a smile to peoples' faces. He...he was my everything. Yes, he was a bit slow but he was so lovely and everyone he met fell in love with him from the start. They always wanted to know where Bobby was or if Bobby wanted to play..." The old woman paused, sniffing slightly before taking a long drawl of her cigarette. "He brought a smile to my face every morning and...and...and now he's go..go..gone." Ms. Mills bit her lip as tears leaked from her eyes and slowly dribbled down her hollowed cheeks. Donna immediately got up and pulled the little old lady into her arms, rocking her back and forth. She silently shushed her and moved her gray hair out of her face. The old woman clutched at Donna's blouse, sobbing as all of her emotions rained down on her. The cigarette laid smoking on the cigarette dish and the Doctor pushed it out of the way to kneel in front of the saddened woman. He placed a comforting hand on her old wrinkled one and slowly rubbed soothing circles on the back.

"Ms. Mills," Donna asked. The little old woman glanced up at the ginger with teary eyes. "Do you know where your son was working?" Ms. Mills shook her head.

"No, I had a bit of an idea because he was spending time with aliens but I never thought twice about it. He was working as a janitor. What could possibly happen?" She replied. Her thin, frail hand reached over to the warm tea and the Doctor passed it over to her. She nodded her thanks before taking a long sip. She gulped loudly, handing it back to the Doctor.

"They told me an alien killed him," the old woman soberly stated. "That the alien shot him in the head with a gun. They said it was you, Doctor." She sighed before continuing. "They dumped his body in this very living room before stomping off and leaving me alone with my dead son." Ms. Mills grabbed her cigarette, puffing out the smoke. Donna rubbed Ms. Mills frail arms in comfort. "I didn't believe them," she muttered, "I heard to many wonderful things about you two and I couldn't imagine you shooting him..." She blew out more smoke, coughing. "And the way they dumped my son on my living room floor in a body bag was evident enough they were lying." The Doctor nodded his head, sadly glancing down at his hands. "I'm alone now," she continued. "My brother died a couple years ago from a drug overdose, God bless his soul and now Bobby's gone too. I have no one. I don't know if you know how that feels, but it is horrible. No one likes seeing their child die before them." The Doctor nodded his head, patting her once more. Donna was surprised to learn that Bobby's uncle was dead because the way he spoke about his uncle made him seem alive. Maybe that's why Bobby did it. So, his uncle could live on through him.

"I understand," the Doctor replied. He sniffed loudly, wiping the tears from his eyes. "I completely understand." The old woman smiled at him, kissing him on the cheek.

"I can see why Bobby liked you," she responded. "You care about people." The Doctor gave a bitter chuckle and covered his mouth. He gave a nod.

"Yeah," he agreed. "And look where it's gotten me." Donna touched his shoulder, rubbing soothing circles. Her eyes were red rimmed as she watched her best mate and Bobby's mother together. In a way they were kindred spirits. Both were alone in a way and lost their whole family. They had no one to lean on when times got rough and they found different ways to cope with the loneliness. The Doctor traveled, meeting new people and learning about new cultures while Ms. Mills buried herself in her home and smoked to dim the pain. But the pain was always there, a constant haunting in their souls. And as she watched these two people talk, nothing remotely in common except for knowing one person, Bobby Mills, Donna knew alien or human when you lose a loved one or you're somewhat alone in the world, people learn to cope and move on with their lives even if sadness and depression weighs down the heart. She sighed, thinking about her grandfather, who was growing older everyday. Every minute might be his last. The tears prickled in her eyes. She knew she needed to spend more time with her gramps because like her father, he too would pass away and Donna would never get the chance to be with him again.

She covered her mouth, choking down a sob. A soft, cool hand touched her's and Donna glanced over, knowing exactly who it was. The Doctor gave her hand a comforting squeeze and a watery smile. It was weird seeing him cry. He never cried and in the past two months or so, he had cried more times then she could count and it made her sad. He wasn't meant to cry. He was meant to be the happy go lucky Time Lord that found trouble around every corner and to see him sad was surreal. But she knew for a long time that this sadness was lingering in his hearts, just waiting to burst, and it finally decided it was time. She squeezed his hand back, telling him she was fine. He excepted the answer without argument.

Ms. Mills got up from her seat and drifted slowly over to a shelf. She picked up a jar and walked back over to the Doctor, holding out the jar for the two to see.

"This is Bobby," she stated, "I had him cremated so I could spread his ashes everywhere he ever was or wanted to be. But the problem is, I don't know where he wanted to go. I'm getting too old to go places and since you two were his friends, I was wondering if you could take him." The Doctor nodded his head, taking the jar. He placed it on the table and pulled the old woman into a hug.

"I know exactly where he wanted to go," the Doctor said. Ms. Mills nodded her head a teardrop trailing down her face.

"Thank you," she said. The Doctor nodded his head and pulled out of the hug. He slowly turned away, picking up the jar. Donna hugged the elderly woman as well, whispering goodbye into her ear. The old woman patted her on the cheek and smiled. Donna followed the Doctor back out onto the streets.

* * *

The Doctor stood at the entrance of his TARDIS, Bobby's ashes wrapped in his arms. Donna stood next to him, leaning her head on his shoulder.

"Well, Bobby, you wanted to see the universe," the Doctor said, "Well here it is." He threw open the TARDIS doors as the Old Girl slowly twirled through space. The stars were splattered across the sky and moons orbited their planets as a bright sun shone from a distance. "Isn't it beautiful Bobby?" the Doctor choked out. "All the stars and planets and life just waiting to be explored." The Doctor held back a sob. "I was going to show you the universe, Bobby. But you died before I got a chance to keep my promise."

Donna stroked the Doctor's arm, humming softly as tears trailed down her face. She looked at the jar holding Bobby's ashes. The Doctor let out a mournful whimper. "So, now I'm going to make sure you're a part of the universe forever. Rest in peace my dear friend and travel throughout the stars." The Doctor opened the jar that held the gray ashes...Bobby's ashes. He threw the ashes off the TARDIS and the ashes floated through space, spreading out among the stars.

"He's now one with the universe," Donna stated, "He will never be forgotten." The Doctor nodded his head and threw his arms around Donna, sobbing into her shoulder. Donna brought him back into the TARDIS and led him towards the console. The Old Girl closed her doors and dimmed the lights, creating a more peaceful surrounding. The two friends cried in each others arms, holding close as they mournfully wept for their fallen friend. Donna was the first to look up. She smoothed back the Doctor's hair, a grim smile on her face.

"Doctor," Donna stated, "I think it's time that we went home." The Doctor glanced up confused.

"But Donna we are home," he said. Donna shook her head.

"No, I meant 2009," she replied. "I miss my family and I want..." The Doctor moved away from her as if he had been slapped. He looked at her with horror and betrayal.

"You want to leave me," he cried. He backed away as she reached out a hand, moving towards the console. "I thought you said...I thought..."

"No, Spaceman that's not what I meant," she responded. "I just meant..."

"No!" he shouted, "I know exactly what you meant! Fine, I'll drop you off at home. You can go back to your temping. I don't need anyone!" He turned away and began flipping switches and turning dials, before he pulled the lever. The TARDIS shook as she threw herself through the time vortex.

"Doctor listen to me," Donna shouted, "You daft martian! You didn't let me finish..."

"No!" he shouted, turning quickly away. "I don't need you or anyone. I'm fine on my own. I'm great on my own!" Donna stomped her foot in frustration as she held tightly onto the railings.

"Come with me you idiot," Donna shouted over the whirring engine. "You're unstable and need people who care around you. Please live with me and my family for a while! We can find Jack or Martha or Sarah Jane and they can help you as well. You need time to relax!"

"No I don't," he shouted stubbornly, a storm brewing behind his eyes. "I'm the Doctor and I don't need you stupid apes or relaxing. There's places to see, people to meet, and bad guys to stop! There's no time for relaxing. I can cope by myself!"

"You're still a person!" Donna shouted, "And even you need to settle down sometimes! You'll burn yourself out or worse get yourself killed! You need your friends. Let me and everyone else help you!"

"Why," he asked. He continued flicking switches and turning knobs.

"Because I care about you," Donna ranted, "You stupid martian and I know you don't believe it, but people actually like you and worry about your safety. So, get off your damn high horse and let me bloody help you!" The Doctor slowed his frantic pacing and glanced at Donna as if Donna had just said the most shocking thing imaginable.

"You really do?" he asked.

"Of course, I bloody do," she exclaimed, "Why do you think I organized the rescue party." The Doctor paused all together and faced Donna. The TARDIS still shook as she flew through the vortex.

"But I don't..." the Doctor began. Donna threw up a hand, stopping his comment.

"Yes you do deserve it," Donna replied, "You deserve every bit of care and love like the next person does. Maybe even more. You've been dealt a terrible hand, Doctor. It's now time to let it go and be with people who love and care about you. It's time for you to slow down and heal." The Doctor bowed his head. He nodded slowly, before turning to the console and clicking a few more buttons with less frantic energy.

"Alright," he said, "I'll come with you." Donna sighed with relief, leaning against the rail. The TARDIS had slowed down, once the Doctor calmed down. This proved how connected the pilot and his ship were. The two travelers flew through the vortex, heading towards there next destination and hopefully this next destination would prove to be the healing both needed.

* * *

**Thanks for all the reviews! I hope you liked this chapter. I know the Doctor's mood swings are irregular and goes between extremely sad to angry but what do you expect from him at this point. He'd been through unimaginable torture at the hands of sadist. He has a right not to be himself. Well, one more chapter to go until this story is over. At the moment I'm trying to figure out how to write these next few stories. So, be patient if the next story is not updated for a while. :) Thanks again for the review and I hope you give me some more wonderful feedback. :)**


	48. analogue

**Thanks for all the wonderful reviews and here is the last chapter. The analogue. Hope you enjoy and read my next few stories when they are written. :)**

Analogue

Four people stood in an abandon lab. Their white lab coats just above the knees. The florescent lights flickered as one of the men stepped forward. He was short with beady black eyes and a hooked nose like a carrionite's. His lab coat looked a lot larger on him then the others, but he was a short man and that was only to be expected when you should be wearing a size small and your lab coat was unfortunately a medium. The man stalked forward towards a large machine. The entrance of the machine was a revolving door and to the side was two panels that took DNA samples. The man pulled out two vials one labeled 'Donna Noble' the other labeled 'Subject 13.' He halted at the machine, a sickly sadistic smile on his lips and his black beady eyes gleamed with wonder. A tall woman with short brown hair and round glasses stepped forward.

"Are you sure it's going to work this time, Dr. Carter,"she asked. Her eyes coldly watched the tiny man. "Because last time was a complete failure with the clone."

"We're not making a clone this time," he responded. His black eyes widened with anticipation. "We're creating a biological baby out of two different sets of DNA. I've done my research and have written out the appropriate formula. I believe we'll be successful this time, my dear Dr. Black."

"But we don't even know if Time Lord DNA and Human DNA will be compatible," Dr. Black argued. "It could have some dangerous side-effects on the fetus if we do it wrong." Dr. Carter shrugged.

"That's why I got some important information from an expert," Dr Carter replied icily. Dr. Sprite and Dr. Berrings watched the two brilliant scientists argue over how to create the fetus. They shrugged their shoulders, taking notes on the process they were going to use.

"What expert," Dr. Black asked indifferently. She set up the machine. Dr. Carter sighed, Placing the vials on the table.

"Remember that strange gray box the soldiers found on the crashed ship a while back and we didn't know what to do with it," Dr. Carter asked. Dr. Black nodded her head. "Well, they discovered this machine on the alien spacecraft as well." He gestured to the large machine, standing tall against the wall. "Well, I was so frustrated trying to figure out what those two objects were because it was something I had never seen before. I almost gave up and threw them away." He picked up the two vials. "Except someone in a cloak came to me one night. It knew exactly what those two objects were. It called the small gray box a Time Distorter. Apparently it was used in some barbaric alien war and was used to destroy or break down ships like that of subject 13's. I immediately told the Colonel and he put it to use." Dr. Carter glanced over at the large metal machine, placing a loving hand on it. "And this, my dear, is called a loom. It was used on the planet that Subject 13 was from to create babies." Dr. Black raised an eyebrow.

"And you know this because?" Dr. Black asked.

"Because this figure...this thing knew more about Subject 13's culture then anybody else," Dr. Carter replied. "It helped set up this place." Dr. Carter motioned around the lab. Dr. Black nodded her head before a shiver ran up her spine. Something was watching her. She just knew it.

"It gave you all this information Carter," Dr. Black said. "But what does it want in return?" A horrendous smile curved Dr. Carters lips.

"Oh, a few alien babies...Specifically Time Lord babies matured at a certain age," Dr. Carter responded. "What it does with them I don't really care. I plan on making a bunch of them anyways. Keeping at least a couple to raise and teach them to serve me as their human master. I will continue what Colonel Graham started. It's a pity UNIT had to come so soon." Dr. Black nodded her head and shrugged. The other two scientists stepped forward, glancing at the DNA in Dr. Carter's hand and the machine.

"What age does it want the babies," she asked.

"Eleven years, I believe," Dr. Carter responded. "It seems to have an interest in Time Lords eleven years or older. It actually took a fancy to subject 13 when it learned we had it." Dr. Black nodded her head. She heard a loud bang from outside, causing her to jump. The whole room had a supernatural feel. Like something was watching from the shadows. Something that was dangerous. Something evil. Dr. Berrings and Dr. Sprite felt the same way. She watched them scoot farther from the shadowed areas of the room, sticking close to the far wall so not to be grabbed from behind. Dr. Carter was the only one oblivious to the deep evils of the room. He was too far gone. He seemed to welcome the darkness.

They heard footsteps coming from down the hall and the four scientists turned as the door creaked open and a familiar woman stepped through. Dr. Morley. Her eyes scrutinized the room nervously as she stepped inside, the floor creaking with every step and a pair of eyes watching her every movement.

"Ah, Dr. Morley,"Dr. Carter exclaimed, "I am relieved you got my message. I'm glad they let you loose. Prison is no place for a woman of your status." Dr. Carter stepped forward, his weaselly face contorted into a sadistic grin.

"What do you want Carter," Morley asked coldly.

"I want your assistance Morley," Dr. Carter stated, "You spoke with Subject 13 and knew how it thought. You can find a way to control our little monsters." She glanced over at the machine that stood against the wall and the DNA vials on the table before glancing back at Carter.

"You're creating Time Lord babies," She stated, "How do you plan on doing that?" Dr. Carter smiled.

"I'll show you if you agree to help me," Carter stated, holding up the two vials. He walked over to the machine, taking the vial tops off.

Dr. Morley pursed her lips. She didn't agree with what this man was doing. Whatever Dr. Carter had planned for the infants was going to be cruel and she worried for the infants safety once they were created. But Morley was a scientist and she wanted to know what made a Time Lord baby's mental development different from a human's and so she agreed with Dr. Carters plan.

"Fine," she said, she placed her hands behind her back, crossing her fingers. "I'll help you." Dr. Carter's grin widened to that of unrealistic lengths.

"Excellent," He stated, "Shall we begin. We'll use about one fourth of the human DNA I collected, meaning the offspring will mostly be Time Lord." He hummed with delight. "Can you imagine the power that will come from these alien offsprings." Dr. Black nodded her head, notepad in hand.

"How long will the development take," Dr. Black asked. Dr. Morley watched Carter's reaction curiously, observing his facial expressions. The other two scientists watched him dump the DNA on the trays.

"The regular nine months maybe. Depends on how long it takes a Time Lord to develop," Dr. Carter stated. "Sadly the loom only produces one baby at a time, so we'll have to keep the DNA we have safe." Dr. Black nodded her head as she jotted down the new information. Dr. Carter stepped over to a computer database, typing in some numbers.

"This machine is quite incredible actually," he commented, "It can decide how much DNA to extract from each sample. All I have to do is type in the percentages of how much DNA I want from each parent and it calculates it before taking the needed amount."

"Impressive," Dr. Morley replied icily. Her eyes kept flitting over towards Carter, who seemed to be growing more excited by the minute. "It must have been an extremely intelligent race of alien." Dr. Black shot her a glare before scoffing.  
"Ladies and gentlemen, this is the beginning of a new species," Dr. Carter announced, "And you'll be the first to witness." Dr. Carter stuck the DNA into the scanner and the machine roared to life as numbers began flashing on the screen and bright lights flashed as the machine took the samples. Dr. Carter stood a satisfied grin on his twisted face.

* * *

**I hope you enjoyed the last chapter. :) Everything will connect together by the third story. :) On another note, I promised to give a quick peek of what to expect for the next story. I've decided to call it Home with the Nobles and it is basically about the Doctor and Donna's healing process. I'm considering doing a bunch of plotless one-shots to take a look at how the Doctor is healing and different fears and traumas he may be facing. The first chapter will start with the Doctor and Donna arriving and the reaction of Sylvia and Wilf and then there on different tales, hurt/comfort, angst, friendship, humor, and other genres to show how the Doctor is surviving domestics. The last chapter will lead into the next story which I will tell you at the end of Home with the Nobles. I'm still trying to decide if there should be a mystery weaved into it or just glimpses of what the Doctor is going through. I haven't decided. If you have anything you want to see, just tell me in a review or PM me. Thank you again for following this story and reviewing. Now I have to plot out the next few stories. I have a basic idea of what I want, but figuring out how I should write it is difficult and will probably drive me mad, until I have some brilliant realization in the middle of the night on how it should be written. Yes, that's what happened with the Underground. Talk about not being able to fall asleep for a few hours and then afterwords to excited to even rest your eyes. Updates this time around may take longer since I will be working and going to school, so hopefully I can update a couple times a week. :) Again thank you for your reviews and I hope you follow into the next few stories. :)**


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